Repeta Daniel J.

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Repeta

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Daniel J.

ORCID

0000-0003-1927-0599

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Biogeochemical relationships between ultrafiltered dissolved organic matter and picoplankton activity in the Eastern Mediterranean Sea

( 2009-12-10) Meador, Travis B. ; Gogou, Alexandra ; Spyres, Georgina ; Herndl, Gerhard J. ; Krasakopoulou, Evangelia ; Psarra, Stella ; Yokokawa, Taichi ; De Corte, Daniele ; Zervakis, Vassilis ; Repeta, Daniel J.

We targeted the warm, subsurface waters of the Eastern Mediterranean Sea (EMS) to investigate processes that are linked to the chemical composition and cycling of dissolved organic carbon (DOC) in seawater. The apparent respiration of semi-labile DOC accounted for 27 ± 18% of oxygen consumption in EMS mesopelagic and bathypelagic waters; this value is higher than that observed in the bathypelagic open ocean, so the chemical signals that accompany remineralization of DOC may thus be more pronounced in this region. Ultrafiltered dissolved organic matter (UDOM) collected from four deep basins at depths ranging from 2 to 4350 m exhibited bulk chemical (1H-NMR) and molecular level (amino acid and monosaccharide) abundances, composition, and spatial distribution that were similar to previous reports, except for a sample collected in the deep waters of the N. Aegean Sea that had been isolated for over a decade. The amino acid component of UDOM was tightly correlated with apparent oxygen utilization and prokaryotic activity, indicating its relationship with remineralization processes that occur over a large range of timescales. Principal component analyses of relative mole percentages of monomers revealed that oxygen consumption and prokaryotic activity were correlated with variability in amino acid distributions but not well correlated with monosaccharide distributions. Taken together, this study elucidates key relationships between the chemical composition of DOM and heterotrophic metabolism.
Phosphonate cycling supports methane and ethylene supersaturation in the phosphate-depleted western North Atlantic Ocean

(Wiley, 2020-05-20) Sosa, Oscar A. ; Burrell, Timothy J. ; Wilson, Samuel T. ; Foreman, Rhea K. ; Karl, David M. ; Repeta, Daniel J.

In oligotrophic ocean regions, dissolved organic phosphorus (DOP) plays a prominent role as a source of phosphorus (P) to microorganisms. An important bioavailable component of DOP is phosphonates, organophosphorus compounds with a carbon‐phosphorus (C‐P) bond, which are ubiquitous in high molecular weight dissolved organic matter (HMWDOM). In addition to being a source of P, the degradation of phosphonates by the bacterial C‐P lyase enzymatic pathway causes the release of trace hydrocarbon gases relevant to climate and atmospheric chemistry. In this study, we investigated the roles of phosphate and phosphonate cycling in the production of methane (CH4) and ethylene (C2H4) in the western North Atlantic Ocean, a region that features a transition in phosphate concentrations from coastal to open ocean waters. We observed an inverse relationship between phosphate and the saturation state of CH4 and C2H4 in the water column, and between phosphate and the relative abundance of the C‐P lyase marker gene phnJ . In phosphate‐depleted waters, methylphosphonate and 2‐hydroxyethylphosphonate, the C‐P lyase substrates that yield CH4 and C2H4, respectively, were readily degraded in proportions consistent with their abundance and bioavailability in HMWDOM and with the concentrations of CH4 and C2H4 in the water column. We conclude that phosphonate degradation through the C‐P lyase pathway is an important source and a common production pathway of CH4 and C2H4 in the phosphate‐depleted surface waters of the western North Atlantic Ocean and that phosphate concentration can be an important control on the saturation state of these gases in the upper ocean.
An extended siderophore suite from Synechococcus sp. PCC 7002 revealed by LC-ICPMS-ESIMS

( 2015-03-11) Boiteau, Rene M. ; Repeta, Daniel J.

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.
Towards integrating evolution, metabolism, and climate change studies of marine ecosystems

(Elsevier, 2019-07-24) Baltar, Federico ; Bayer, Barbara ; Bednarsek, Nina ; Deppeler, Stacy ; Escribano, Ruben ; Gonzalez, Carolina E. ; Hansman, Roberta L. ; Mishra, Rajani Kanta ; Moran, Mary Ann ; Repeta, Daniel J. ; Robinson, Carol ; Sintes, Eva ; Tamburini, Christian ; Valentin, Luis E. ; Herndl, Gerhard J.

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.
Ultrasonic nebulization for the elemental analysis of microgram-level samples with offline aerosol mass spectrometry

(European Geosciences Union, 2019-03-14) O'Brien, Rachel E. ; Ridley, Kelsey J. ; Canagaratna, Manjula R. ; Jayne, John T. ; Croteau, Philip L. ; Worsnop, Douglas R. ; Budisulistiorini, Sri Hapsari ; Surratt, Jason D. ; Follett, Christopher L. ; Repeta, Daniel J. ; Kroll, Jesse H.

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 matter.
Seasonal occurrence of anoxygenic photosynthesis in Tillari and Selaulim reservoirs, Western India

(Copernicus Publications on behalf of the European Geosciences Union, 2012-07-09) Kurian, S. ; Roy, Rajdeep ; Repeta, Daniel J. ; Gauns, M. U. ; Shenoy, D. M. ; Suresh, T. ; Sarkar, A. ; Narvenkar, G. ; Johnson, Carl G. ; Naqvi, S. W. A.

Phytoplankton and bacterial pigment compositions were determined by high performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS) in two freshwater reservoirs (Tillari Dam and Selaulim Dam), which are located at the foothills of the Western Ghats in India. These reservoirs experience anoxia in the hypolimnion during summer. Water samples were collected from both reservoirs during anoxic periods while one of them (Tillari Reservoir) was also sampled in winter, when convective mixing results in well-oxygenated conditions throughout the water column. During the period of anoxia (summer), bacteriochlorophyll (BChl) e isomers and isorenieratene, characteristic of brown sulfur bacteria, were dominant in the anoxic (sulfidic) layer of the Tillari Reservoir under low light intensities. The winter observations showed the dominance of small cells of Chlorophyll b-containing green algae and cyanobacteria, with minor presence of fucoxanthin-containing diatoms and peridinin-containing dinoflagellates. Using total BChl e concentration observed in June, the standing stock of brown sulfur bacteria carbon in the anoxic compartment of Tillari Reservoir was estimated to be 2.27 gC m−2, which is much higher than the similar estimate for carbon derived from oxygenic photosynthesis (0.82 gC m−2. The Selaulim Reservoir also displayed similar characteristics with the presence of BChl e isomers and isorenieratene in the anoxic hypolimnion during summer. Although sulfidic conditions prevailed in the water column below the thermocline, the occurrence of photo-autotrophic bacteria was restricted only to mid-depths (maximal concentration of BChl e isomers was detected at 0.2% of the surface incident light). This shows that the vertical distribution of photo-autotrophic sulfur bacteria is primarily controlled by light penetration in the water column where the presence of H2S provides a suitable biogeochemical environment for them to flourish.
Dissolved organic nitrogen hydrolysis rates in axenic cultures of Aureococcus anophagefferens (Pelagophyceae) : comparison with heterotrophic bacteria

(American Society for Microbiology, 2002-01) Berg, Gry M. ; Repeta, Daniel J. ; LaRoche, Julie

The marine autotroph Aureococcus anophagefferens (Pelagophyceae) was rendered axenic in order to investigate hydrolysis rates of peptides, chitobiose, acetamide, and urea as indicators of the ability to support growth on dissolved organic nitrogen. Specific rates of hydrolysis varied between 8 and 700% of rates observed in associated heterotrophic marine bacteria.
Transformations of carotenoids in the oceanic water column

(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 1982-08) Repeta, Daniel J.

In an effort to understand the more general mechanisms and rates of pre-depositional reactions that transform organic matter, the types and relevant time scales of reactions that transform carotenoid pigments in the oceanic water column were studied. Suspended particulate matter collected from surface waters of Buzzards Bay, Massachusetts and the Peru upwelling system has a carotenoid distribution reflecting the phytoplanktonic source of the material. The carotenoid distribution of sediment trap samples collected in these same areas was dominated by transformation products. Fucoxanthin, the primary carotenoid of marine diatoms, typically constituted 77-100% of the total fucopigments in suspended particulate material. In sediment trap samples this pigment constituted only 4-85% of the total. The remaining 15-96% of the pigments consisted of the fucoxanthin transformations products: free alcohols (2-94%), dehydrates (0-6%), and opened epoxides (0-19%). Preliminary results suggest that carotenoid esters are hydrolyzed to free alcohols at a rate determined by the turnover of primary productivity. The dehydrated and epoxide opened intermediates of fucoxanthin represent products of transformation reactions that operate over much longer time scales (0.1-10 yrs). Dehydration and epoxide opening are not significant water column transformations, but are important in surface sediments.
Concentration measurements of water column phosphate, nitrate and nitrite, dissolved organic phosphorus, methane, and ethylene from samples collected during the R/V Neil Armstrong cruise AR16 in the western North Atlantic Ocean in May 2017

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-07-22) Repeta, Daniel J. ; Karl, David M.

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
Isolation and characterization of bacteria that degrade phosphonates in marine dissolved organic matter

(Frontiers Media, 2017-09-26) Sosa, Oscar A. ; Repeta, Daniel J. ; Ferrón, Sara ; Bryant, Jessica A. ; Mende, Daniel R. ; Karl, David M. ; DeLong, Edward F.

Semi-labile dissolved organic matter (DOM) accumulates in surface waters of the oligotrophic ocean gyres and turns over on seasonal to annual timescales. This reservoir of DOM represents an important source of carbon, energy, and nutrients to marine microbial communities but the identity of the microorganisms and the biochemical pathways underlying the cycling of DOM remain largely uncharacterized. In this study we describe bacteria isolated from the North Pacific Subtropical Gyre (NPSG) near Hawaii that are able to degrade phosphonates associated with high molecular weight dissolved organic matter (HMWDOM), which represents a large fraction of semi-labile DOM. We amended dilution-to-extinction cultures with HMWDOM collected from NPSG surface waters and with purified HMWDOM enriched with polysaccharides bearing alkylphosphonate esters. The HMWDOM-amended cultures were enriched in Roseobacter isolates closely related to Sulfitobacter and close relatives of hydrocarbon-degrading bacteria of the Oceanospirillaceae family, many of which encoded phosphonate degradation pathways. Sulfitobacter cultures encoding C-P lyase were able to catabolize methylphosphonate and 2-hydroxyethylphosphonate, as well as the esters of these phosphonates found in native HMWDOM polysaccharides to acquire phosphorus while producing methane and ethylene, respectively. Conversely, growth of these isolates on HMWDOM polysaccharides as carbon source did not support robust increases in cell yields, suggesting that the constituent carbohydrates in HMWDOM were not readily available to these individual isolates. We postulate that the complete remineralization of HMWDOM polysaccharides requires more complex microbial inter-species interactions. The degradation of phosphonate esters and other common substitutions in marine polysaccharides may be key steps in the turnover of marine DOM.
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.
Structural characterization of natural nickel and copper binding ligands along the US GEOTRACES Eastern Pacific Zonal Transect

(Frontiers Media, 2016-11-30) Boiteau, Rene M. ; Till, Claire P. ; Ruacho, Angel ; Bundy, Randelle M. ; Hawco, Nicholas J. ; McKenna, Amy M. ; Barbeau, Katherine A. ; Bruland, Kenneth W. ; Saito, Mak A. ; Repeta, Daniel J.

Organic ligands form strong complexes with many trace elements in seawater. Various metals can compete for the same ligand chelation sites, and the final speciation of bound metals is determined by relative binding affinities, concentrations of binding sites, uncomplexed metal concentrations, and association/dissociation kinetics. Different ligands have a wide range of metal affinities and specificities. However, the chemical composition of these ligands in the marine environment remains poorly constrained, which has hindered progress in modeling marine metal speciation. In this study, we detected and characterized natural ligands that bind copper (Cu) and nickel (Ni) in the eastern South Pacific Ocean with liquid chromatography tandem inductively coupled plasma mass spectrometry (LC-ICPMS), and high-resolution electrospray ionization mass spectrometry (ESIMS). Dissolved Cu, Ni, and ligand concentrations were highest near the coast. Chromatographically unresolved polar compounds dominated ligands isolated near the coast by solid phase extraction. Offshore, metal and ligand concentrations decreased, but several new ligands appeared. One major ligand was detected that bound both Cu2+ and Ni2+. Based on accurate mass and fragmentation measurements, this compound has a molecular formula of [C20H21N4O8S2+M]+ (M = metal isotope) and contains several azole-like metal binding groups. Additional lipophilic Ni complexes were also present only in oligotrophic waters, with masses of 649, 698, and 712 m/z (corresponding to the 58Ni metal complex). Molecular formulae of [C32H54N3O6S2Ni]+ and [C33H56N3O6S2Ni]+ were determined for two of these compounds. Addition of Cu and Ni to the samples also revealed the presence of additional compounds that can bind both Ni and Cu. Although these specific compounds represent a small fraction of the total dissolved Cu and Ni pool, they highlight the compositional diversity and spatial heterogeneity of marine Ni and Cu ligands, as well as variability in the extent to which different metals in the same environment compete for ligand binding.
Revisiting the pink-red pigmented basidiomycete mirror yeast of the phyllosphere

(John Wiley & Sons, 2016-05-10) Cobban, Alec ; Edgcomb, Virginia P. ; Burgaud, Gaëtan ; Repeta, Daniel J. ; Leadbetter, Edward R.

By taking advantage of the ballistoconidium-forming capabilities of members of the genus Sporobolomyces, we recovered ten isolates from deciduous tree leaves collected from Vermont and Washington, USA. Analysis of the small subunit ribosomal RNA gene and the D1/D2 domain of the large subunit ribosomal RNA gene indicate that all isolates are closely related. Further analysis of their physiological attributes shows that all were similarly pigmented yeasts capable of growth under aerobic and microaerophilic conditions, all were tolerant of repeated freezing and thawing, minimally tolerant to elevated temperature and desiccation, and capable of growth in liquid or on solid media containing pectin or galacturonic acid. The scientific literature on ballistoconidium-forming yeasts indicates that they are a polyphyletic group. Isolates of Sporobolomyces from two geographically separated sites show almost identical phenotypic and physiological characteristics and a monophyly with a broad group of differently named Sporobolomyces/Sporidiobolus species based on both small subunit ribosomal RNA (SSU rRNA) and D1/D2 domains of the LSU rRNA gene sequences.
Deciphering ocean carbon in a changing world

( 2016-01-13) Moran, Mary Ann ; Kujawinski, Elizabeth B. ; Stubbins, Aron ; Fatland, Rob ; Aluwihare, Lihini I. ; Buchan, Alison ; Crump, Byron C. ; Dorrestein, Pieter C. ; Dyhrman, Sonya T. ; Hess, Nancy J. ; Howe, Bill ; Longnecker, Krista ; Medeiros, Patricia M. ; Niggemann, Jutta ; Obernosterer, Ingrid ; Repeta, Daniel J. ; Waldbauer, Jacob R.

Dissolved organic matter (DOM) in the oceans is one of the largest pools of reduced carbon on Earth, comparable in size to the atmospheric CO2 reservoir. A vast number of compounds are present in DOM and they play important roles in all major element cycles, contribute to the storage of atmospheric CO2 in the ocean, support marine ecosystems, and facilitate interactions between organisms. At the heart of the DOM cycle lie molecular-level relationships between the individual compounds in DOM and the members of the ocean microbiome that produce and consume them. In the past, these connections have eluded clear definition because of the sheer numerical complexity of both DOM molecules and microorganisms. Emerging tools in analytical chemistry, microbiology and informatics are breaking down the barriers to a fuller appreciation of these connections. Here we highlight questions being addressed using recent methodological and technological developments in those fields and consider how these advances are transforming our understanding of some of the most important reactions of the marine carbon cycle.
Element-selective targeting of nutrient metabolites in environmental samples by inductively coupled plasma mass spectrometry and electrospray ionization mass spectrometry

(Frontiers Media, 2021-03-13) Li, Jingxuan ; Boiteau, Rene M. ; Babcock-Adams, Lydia ; Song, Zhongchang ; McIlvin, Matthew R. ; Repeta, Daniel J.

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.
Iron depletion in the deep chlorophyll maximum: mesoscale eddies as natural iron fertilization experiments

(American Geophysical Union, 2021-11-17) Hawco, Nicholas J. ; Barone, Benedetto ; Church, Matthew J. ; Babcock-Adams, Lydia ; Repeta, Daniel J. ; Wear, Emma K. ; Foreman, Rhea K. ; Björkman, Karin M. ; Bent, Shavonna M. ; Van Mooy, Benjamin A. S. ; Sheyn, Uri ; DeLong, Edward F. ; Acker, Marianne ; Kelly, Rachel L. ; Nelson, Alexa ; Ranieri, John ; Clemente, Tara M. ; Karl, David M. ; John, Seth G.

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.
Seasonal and annual fluxes of nutrients and organic matter from large rivers to the Arctic Ocean and surrounding seas

( 2011-03) Holmes, Robert M. ; McClelland, James W. ; Peterson, Bruce J. ; Tank, Suzanne E. ; Bulygina, Ekaterina ; Eglinton, Timothy I. ; Gordeev, Viacheslav V. ; Gurtovaya, Tatiana Y. ; Raymond, Peter A. ; Repeta, Daniel J. ; Staples, Robin ; Striegl, Robert G. ; Zhulidov, Alexander V. ; Zimov, Sergey A.

River inputs of nutrients and organic matter impact the biogeochemistry of arctic estuaries and the Arctic Ocean as a whole, yet there is considerable uncertainty about the magnitude of fluvial fluxes at the pan-arctic scale. Samples from the six largest arctic rivers, with a combined watershed area of 11.3 x 106 km2, have revealed strong seasonal variations in constituent concentrations and fluxes within rivers as well as large differences among the rivers. Specifically, we investigate fluxes of dissolved organic carbon, dissolved organic nitrogen, total dissolved phosphorus, dissolved inorganic nitrogen, nitrate, and silica. This is the first time that seasonal and annual constituent fluxes have been determined using consistent sampling and analytical methods at the pan arctic scale, and consequently provide the best available estimates for constituent flux from land to the Arctic Ocean and surrounding seas. Given the large inputs of river water to the relatively small Arctic Ocean, and the dramatic impacts that climate change is having in the Arctic, it is particularly urgent that we establish the contemporary river fluxes so that we will be able to detect future changes and evaluate the impact of the changes on the biogeochemistry of the receiving coastal and ocean systems.
Bacterial quorum-sensing signal arrests phytoplankton cell division and impacts virus-induced mortality

(American Society for Microbiology, 2021-05-12) Pollara, Scott B. ; Becker, Jamie W. ; Nunn, Brook L. ; Boiteau, Rene M. ; Repeta, Daniel J. ; Mudge, Miranda C. ; Downing, Grayton ; Chase, Davis ; Harvey, Elizabeth L. ; Whalen, Kristen E.

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.
Understanding the role of the biological pump in the global carbon cycle : an imperative for ocean science

(The Oceanography Society, 2014-09) Honjo, Susumu ; Eglinton, Timothy I. ; Taylor, Craig D. ; Ulmer, Kevin M. ; Sievert, Stefan M. ; Bracher, Astrid ; German, Christopher R. ; Edgcomb, Virginia P. ; Francois, Roger ; Iglesias-Rodriguez, M. Debora ; Van Mooy, Benjamin A. S. ; Repeta, Daniel J.

Anthropogenically driven climate change will rapidly become Earth's dominant transformative influence in the coming decades. The oceanic biological pump—the complex suite of processes that results in the transfer of particulate and dissolved organic carbon from the surface to the deep ocean—constitutes the main mechanism for removing CO2 from the atmosphere and sequestering carbon at depth on submillennium time scales. Variations in the efficacy of the biological pump and the strength of the deep ocean carbon sink, which is larger than all other bioactive carbon reservoirs, regulate Earth's climate and have been implicated in past glacial-interglacial cycles. The numerous biological, chemical, and physical processes involved in the biological pump are inextricably linked and heterogeneous over a wide range of spatial and temporal scales, and they influence virtually the entire ocean ecosystem. Thus, the functioning of the oceanic biological pump is not only relevant to the modulation of Earth's climate but also constitutes the basis for marine biodiversity and key food resources that support the human population. Our understanding of the biological pump is far from complete. Moreover, how the biological pump and the deep ocean carbon sink will respond to the rapid and ongoing anthropogenic changes to our planet—including warming, acidification, and deoxygenation of ocean waters—remains highly uncertain. To understand and quantify present-day and future changes in biological pump processes requires sustained global observations coupled with extensive modeling studies supported by international scientific coordination and funding.
Sampling of basement fluids via circulation obviation retrofit kits (CORKs) for dissolved gases, fluid fixation at the seafloor, and the characterization of organic carbon

(Elsevier, 2020-08-15) Lin, Huei-Ting ; Hsieh, Chih-Chiang ; Repeta, Daniel J. ; Rappe, Michael S.

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.

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