Daniel J. Repeta

Woods Hole Oceanographic Institution, Falmouth, Massachusetts, United States

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Publications (49)195.93 Total impact

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    ABSTRACT: Dissolved organic matter (DOM) is the largest active organic carbon reservoir in the ocean (662 GT C), a major fraction (> 95%) of which remains chemically uncharacterized. The concentration and isolation of DOM from seawater by ultrafiltration facilitates its chemical characterization by spectroscopic techniques. Using ultrafiltration, silver cation preparative chromatography and gas chromatography coupled with mass spectrometry (GC–MS), we identified 50 novel sugar compounds after hydrolysis of the high molecular weight dissolved organic matter fraction (HMWDOM; the fraction of DOM isolated after ultrafiltration). Sugars were identified by comparison of their mass spectra with those of chemically synthetized standards and with spectra previously described in the literature. Our results showed that mono- and di-methylated hexoses; mono- and di-methylated pentoses; mono- and di-methylated 6-deoxysugars, as well as heptoses, methylated heptoses, 3,6-dideoxysugars and 1,6 anhydrosugars (levoglucosan, mannosan, and galactosan) are components of HMWDOM, which may explain the low apparent yields of sugars recovered by molecular level (HPLC) analyses of HMWDOM after hydrolysis.From three depths spanning the surface (15 m) to bathypelagic (1800 m) ocean in the North Pacific near Hawaii our results showed that mono- and di-methylated hexoses were most abundant in the surface sample (64% of the total identified methylated sugar compounds), while at 1800 m monomethylated 6-deoxysugars were the dominant sugars (42% of the total identified methylated sugar compounds). The high diversity of mono- and di-methylated hexoses in the surface sample most likely suggests an algal and/or bacterial source, while the high abundance of methylated 6-deoxy hexoses in the deep sample points toward an important bacterial contribution because the latter sugars are mostly found in bacterial lipopolysaccharides as well as highly degraded organic material.
    Marine Chemistry 11/2013; 154:34–45. · 3.00 Impact Factor
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    ABSTRACT: A considerable fraction of the Earth's organic carbon exists in dissolved form in seawater. To investigate the roles of planktonic marine microbes in the biogeochemical cycling of this dissolved organic matter (DOM), we performed controlled seawater incubation experiments and followed the responses of an oligotrophic surface water microbial assemblage to perturbations with DOM derived from an axenic culture of Prochlorococcus, or high-molecular weight DOM concentrated from nearby surface waters. The rapid transcriptional responses of both Prochlorococcus and Pelagibacter populations suggested the utilization of organic nitrogen compounds common to both DOM treatments. Along with these responses, both populations demonstrated decreases in gene transcripts associated with nitrogen stress, including those involved in ammonium acquisition. In contrast, responses from low abundance organisms of the NOR5/OM60 gammaproteobacteria were observed later in the experiment, and included elevated levels of gene transcripts associated with polysaccharide uptake and oxidation. In total, these results suggest that numerically dominant oligotrophic microbes rapidly acquire nitrogen from commonly available organic sources, and also point to an important role for carbohydrates found within the DOM pool for sustaining the less abundant microorganisms in these oligotrophic systems.
    Environmental Microbiology 08/2013; · 5.76 Impact Factor
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    ABSTRACT: Plant wax lipids and lignin phenols are the two most common classes of molecular markers that are used to trace vascular plant-derived OM in the marine environment. However, their 13C and 14C compositions have not been directly compared, which can be used to constrain the flux and attenuation of terrestrial carbon in marine environment. In this study, we describe a revised method of isolating individual lignin phenols from complex sedimentary matrices for 14C analysis using high pressure liquid chromatography (HPLC) and compare this approach to a method utilizing preparative capillary gas chromatography (PCGC). We then examine in detail the 13C and 14C compositions of plant wax lipids and lignin phenols in sediments from the inner and mid shelf of the Washington margin that are influenced by discharge of the Columbia River. Plant wax lipids (including n-alkanes, n-alkanoic (fatty) acids, n-alkanols, and n-aldehydes) displayed significant variability in both δ13C (‒28.3 to ‒37.5 ‰) and ∆14C values (‒204 to +2 ‰), suggesting varied inputs and/or continental storage and transport histories. In contrast, lignin phenols exhibited similar δ13C values (between ‒30 to ‒34 ‰) and a relatively narrow range of ∆14C values (‒45 to ‒150 ‰; HPLC-based mesurement) that were similar to, or younger than, bulk OM (‒195 to ‒137 ‰). Moreover, lignin phenol 14C age correlated with the degradation characteristics of this terrestrial biopolymer in that vanillyl phenols were on average ~500 years older than syringyl and cinnamyl phenols that degrade faster in soils and sediments. The isotopic characteristics, abundance, and distribution of lignin phenols in sediments suggest that they serve as promising tracers of recently biosynthesized terrestrial OM during supply to, and dispersal within the marine environment. Lignin phenol 14C measurements may also provide useful constraints on the vascular plant end member in isotopic mixing models for carbon source apportionment, and for interpretation of sedimentary records of past vegetation dynamics.
    Geochimica et Cosmochimica Acta 04/2013; 105:14-30. · 3.88 Impact Factor
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    ABSTRACT: The aim of this study was to investigate the chemical composition and cycling of dissolved organic matter (DOM), focusing on the influence of thermal stratification and mixing. Samples were collected at the surface, 500 m and 1500 m, in April, July and October 2004 at the DYFAMED time-series site in the Northwestern Mediterranean. High molecular weight (HMW) DOM was concentrated using ultrafiltration. The HMW DOM fraction was characterised by 1H NMR, amino acid and neutral sugar analysis. Results were interpreted in the context of the wealth of information available on site DYFAMED. Three key observations were made. Firstly, the carbohydrate component of DOM decreased with depth, in agreement with previous studies, indicating degradation of this labile material. Secondly, the July surface water sample was particularly carbohydrate rich; it is proposed this may be the result of increased carbohydrate production by phytoplankton under low nutrient conditions, and accumulation in the surface layers due to stratification of the water column. Finally, the October samples showed a distinctly different chemical signature to the April and July samples, potentially indicating a shift from a net production system in the spring and summer to a net re-mineralisation system in autumn. The results of this study offer an insight into the dynamic nature of DOM at station DYFAMED.
    Progress In Oceanography 01/2013; 119:78–89. · 3.71 Impact Factor
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    ABSTRACT: 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 × 106km2, 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. KeywordsArctic–Rivers–Arctic rivers–Siberia–Land–ocean linkage–Climate change–Permafrost–Dissolved organic carbon–DOC
    Estuaries and Coasts 03/2012; 35(2):369-382. · 2.56 Impact Factor
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    ABSTRACT: Marine dissolved organic matter (DOM) contains as much carbon as the Earth's atmosphere, and represents a critical component of the global carbon cycle. To better define microbial processes and activities associated with marine DOM cycling, we analyzed genomic and transcriptional responses of microbial communities to high-molecular-weight DOM (HMWDOM) addition. The cell density in the unamended control remained constant, with very few transcript categories exhibiting significant differences over time. In contrast, the DOM-amended microcosm doubled in cell numbers over 27 h, and a variety of HMWDOM-stimulated transcripts from different taxa were observed at all time points measured relative to the control. Transcripts significantly enriched in the HMWDOM treatment included those associated with two-component sensor systems, phosphate and nitrogen assimilation, chemotaxis, and motility. Transcripts from Idiomarina and Alteromonas spp., the most highly represented taxa at the early time points, included those encoding TonB-associated transporters, nitrogen assimilation genes, fatty acid catabolism genes, and TCA cycle enzymes. At the final time point, Methylophaga rRNA and non-rRNA transcripts dominated the HMWDOM-amended microcosm, and included gene transcripts associated with both assimilatory and dissimilatory single-carbon compound utilization. The data indicated specific resource partitioning of DOM by different bacterial species, which results in a temporal succession of taxa, metabolic pathways, and chemical transformations associated with HMWDOM turnover. These findings suggest that coordinated, cooperative activities of a variety of bacterial "specialists" may be critical in the cycling of marine DOM, emphasizing the importance of microbial community dynamics in the global carbon cycle.
    Proceedings of the National Academy of Sciences 09/2010; 107(38):16420-7. · 9.74 Impact Factor
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    Alexandra Gogou, Daniel J. Repeta
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    ABSTRACT: Chemical characterizations of high molecular weight dissolved organic matter (HMW DOM) have shown that a compositionally well-defined family of acylated polysaccharides (APS) contributes a large fraction of DOM in the surface ocean. One process that might affect APS cycling is physical removal by aggregation. To investigate the importance of this mechanism, we compared the chemical composition and transparent exopolymer particle (TEP) abundances of seawater HMW DOM with surface-active organic matter (SAOM) that accumulates as standing sea surface foam during intense wind events. We further simulated the aggregation of SAOM using bubble-adsorption of HMW DOM isolated from laboratory cultures of the diatom Chaetoceros neogracile. 1H-NMR spectroscopy and molecular-level analysis of natural and laboratory-produced HMW DOM and SAOM show important contributions from polysaccharides, acetate, and aliphatic organic matter and similar yields and distributions of neutral sugars after hydrolysis. Microbial degradation of Chaetoceros neogracile DOM removes proteins and mannose-rich polysaccharides to produce HMW DOM with spectral and molecular-level characteristics that resemble seawater APS. These results imply that APS and hydrolysable sugars are resistant to microbial degradation over the time frame of our degradation experiment (40days). As revealed by 1H-NMR spectroscopy and by the neutral monosaccharide data, there are important similarities in the composition of APS in HMW DOM and natural and laboratory-produced SAOM foamy material, rich in TEP. Although these samples are operationally classified in two distinct pools (dissolved vs. particulate) in seawater, they exhibit similar chemical and spectral characteristics. Finally, TEP concentration measurements in SAOM samples indicate that freshly-produced diatom DOM yields SAOM with TEP concentration similar to seawater and natural SAOM, but seven times higher than SAOM produced after bubble-adsorption of degraded HMW DOM.
    Marine Chemistry - MAR CHEM. 01/2010; 121(1):215-223.
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    ABSTRACT: 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.
    Deep Sea Research Part II Topical Studies in Oceanography 01/2010; · 2.24 Impact Factor
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    ABSTRACT: A high-resolution sea surface temperature and paleoproductivity reconstruction on a sedimentary record collected at 36°S off central-south Chile (GeoB 7165-1, 36°33′S, 73°40′W, 797 m water depth, core length 750 cm) indicates that paleoceanographic conditions changed abruptly between 18 and 17 ka. Comparative analysis of several cores along the Chilean continental margin (30°–41°S) suggests that the onset and the pattern of deglacial warming was not uniform off central-south Chile due to the progressive southward migration of the Southern Westerlies and local variations in upwelling. Marine productivity augmented rather abruptly at 13–14 ka, well after the oceanographic changes. We suggest that the late deglacial increase in paleoproductivity off central-south Chile reflects the onset of an active upwelling system bringing nutrient-rich, oxygen-poor Equatorial Subsurface Water to the euphotic zone, and a relatively higher nutrient load of the Antarctic Circumpolar Current. During the Last Glacial Maximum, when the Southern Westerlies were located further north, productivity off central-south Chile, in contrast to off northern Chile, was reduced due to direct onshore-blowing winds that prevented coastal upwelling and export production.
    Earth and Planetary Science Letters 01/2008; 272:221-230. · 4.35 Impact Factor
  • Tracy M. Quan, Daniel J. Repeta
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    ABSTRACT: Nuclear magnetic resonance spectroscopy has been used to infer that marine high molecular weight dissolved organic matter (HMWDOM) is a mixture of carbohydrates, proteins, and lipids. However, acid and base catalyzed hydrolysis of HMWDOM followed by molecular level analyses using gas and liquid chromatography provide only low to modest yields of simple sugars, amino acids, and lipids. Here we use periodate over-oxidation to investigate the composition of HMWDOM. Our analyses show that the oxidation of HMWDOM carbohydrate consumes more periodate per carbon on a molar basis (1.3:1) than simple sugars (0.8:1) or linear polysaccharides (1.0:1), and that HMWDOM is highly branched. We also recover acetic acid and methanol as major oxidation products. Methanol and acetic acid are derived from the oxidation of methyl and 6-deoxy sugars, and our analyses suggest these sugars are major components of HMWDOM. Periodate over-oxidation shows that lipids are not major constituents of HMWDOM, and that most of the alkyl carbon observed in the 13CNMR spectra between 0–45 ppm that has been previously assigned to lipids is due to the methyl carbons of acetamide and 6-deoxy sugars.
    Marine Chemistry - MAR CHEM. 01/2007; 105(3):183-193.
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    ABSTRACT: Nuclear magnetic resonance (NMR) spectroscopy shows that > 50% of the carbon in marine high molecular weight dissolved organic matter (HMWDOM) from surface waters is a compositionally well-defined family of acylated polysaccharides that is conserved across ocean basins. However, acid hydrolysis of HMWDOM, followed by chromatographic analysis, recovers only 10–20% of the carbon as neutral, amino and acidic sugars. Most carbohydrate in HMWDOM therefore remains uncharacterized. Here, we use acid hydrolysis followed by Ag+ and Pb2+ cation exchange chromatography to separate HMWDOM hydrolysis products for characterization using 1-D and 2-D NMR spectroscopy. In addition to neutral sugars identified in past studies, we find 3-O-methylglucose, 3-O-methylrhamnose, 2-O-methylrhamnose and 2-O-methylfucose. We also find 3-deoxysugars to be present, although their complete structures could not be determined. Methyl sugars are widely distributed in plant and bacterial structural carbohydrates, such as cell wall polysaccharides, and their presence in HMWDOM suggests that structural carbohydrates may contribute to DOM in surface seawater. We find most HMWDOM carbohydrate is not depolymerized by acid hydrolysis and that the non-hydrolyzable component includes 6-deoxysugars.
    Organic Geochemistry. 01/2007;
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    Daniel J. Repeta, Lihini I. Aluwihare
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    ABSTRACT: We used compound-specific natural-abundance radiocarbon analyses of neutral sugars to study carbon cycling of high-molecular-weight (HMW) dissolved organic carbon (DOC) at two sites in the North Pacific Ocean. Sugars released from HMW DOC by acid hydrolysis were purified by high-pressure liquid chromatography and analyzed for radiocarbon content via accelerator mass spectrometry. The seven most abundant sugars recovered from HMW DOC have similar radiocarbon values, supporting the hypothesis that these sugars are incorporated into a common family of polysaccharides. Neutral sugar D 14 C values from surface waters collected in 1999 and 2001 are 89 6 13‰ and 57 6 6‰, respectively; these values are much more enriched in radiocarbon than those found in previous studies that used operationally defined carbohydrate fractions. Radiocarbon values for HMW DOC neutral sugars are the same as, or only slightly depleted relative to, dissolved inorganic carbon (DIC), which is consistent with rapid cycling and a short (,3-yr) residence time. In addition, the D 14 C value of neutral sugars at 600 m is 20‰ enriched relative to DIC D 14 C, suggesting that a fraction of dissolved neutral sugars at this depth are introduced by dissolution from large, rapidly sinking particles.
    Limnology and Oceanography - LIMNOL OCEANOGR. 01/2006; 51(2):1045-1053.
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    ABSTRACT: A major fraction of particulate organic carbon (POC) in the deep ocean remains molecularly uncharacterized. In an effort to determine the chemical characteristics and source(s) of sinking POC, we studied a nonhydrolyzable fraction of sinking POC using 13C NMR (nuclear magnetic resonance) spectroscopy and analytical pyrolysis. 13C NMR spectra and products from analytical pyrolysis of the nonhydrolyzable fraction exhibit a strongly aliphatic character that is distinct from that of bulk POC. The aliphatic nature of this fraction is consistent with its low stable carbon isotope values. We hypothesize that the nonhydrolyzable fraction derives to a significant extent from a refractory component of organisms that selectively accumulates, resulting in its manifestation as a major part of POC sinking to the deep ocean and in underlying sediments.
    Geochimica et Cosmochimica Acta 01/2006; 70:5162-5168. · 3.88 Impact Factor
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    ABSTRACT: The chemical dynamics of marine dissolved organic nitrogen (DON), a reservoir featuring surface accumulations even in areas where nitrogen limits productivity, have yet to be resolved. We exploited differences in the acid lability of amide bonds within high-molecular-weight (HMW) DON to show that vertical DON profiles result in part from the presence of two chemically distinct pools of amide. Half of HMWDON in surface waters is present as N-acetyl amino polysaccharides. In contrast, nearly all deep-sea HMWDON, and therefore, most HMWDON, is present in amides that resist both chemical hydrolysis and biological degradation.
    Science 06/2005; 308(5724):1007-10. · 31.20 Impact Factor
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    ABSTRACT: Chromophoric or colored dissolved organic matter (CDOM) is one of the principal light adsorbing components of seawater, particularly in the ultraviolet, where it attenuates over 90% of downwelling ultraviolet radiation. In highly productive coastal regions and throughout most of the global ocean, in situ biological production is the major source of CDOM. However, little is known about CDOM composition on the molecular level, and there are only a few reports that link CDOM composition to autochthonous biological sources. Here we report the isolation and characterization of CDOM components from one coastal and two open-ocean sites. Each sample contains a complex mixture of light absorbing (300-400 nm) components, including 2,4-dichlorobenzoic acid and a suite of novel, polychlorinated biphenyl carboxylic acids that closely resemble polychlorinated biphenyls (PCBs) of anthropogenic origin. However, the global inventory and isomer distribution of dissolved chlorinated aromatic acids suggest they are derived from in situ biological production rather than anthropogenic contaminants. These novel chlorinated aromatic acids account for a significant amount of CDOM adsorption in the ultraviolet.
    Environmental Science and Technology 11/2004; 38(20):5373-8. · 5.26 Impact Factor
  • Rubén Ocampo, Daniel J. Repeta
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    ABSTRACT: We report the structure determination (RP-18 HPLC, UV–vis, MS, 1H NMR) of the purified 132(S)–OH methyl bacteriopheophorbide a allomer isolated from a coastal salt pond sediment (Salt Pond, MA, USA). This compound, which occurs with its pheophytin counterpart, is a new bacteriochlorophyll a molecular fossil and may be an intermediate in the formation of some ETIO porphyrins previously isolated from ancient sediments.
    Organic Geochemistry - ORG GEOCHEM. 01/2004; 35(2):209-214.