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Exudates by the diatom Phaeodactylum tricornutum were incubated with a natural community of marine heterotrophic prokaryotes for 24 d in order to investigate the link between the biological lability and the molecular weight, fluorescence, and polarity of phytoplankton dissolved organic matter (DOM). Dissolved organic carbon (DOC) removal, changes in fluorescence and in the heterotrophic prokaryote abundance were followed over time both in the total exudates and in the low‐ and high‐molecular‐weight fractions. To detect changes in the polarity of proteins, reverse‐phase high‐performance liquid chromatography (HPLC) was applied to the high‐molecular‐weight fraction. Our results indicate that freshly produced phytoplankton DOM exhibits a dynamic pattern of degradation that is accompanied by large changes in the growth efficiency of the bacterial community that are likely related to changes in DOM quality. Approximately 20% of high‐molecular‐weight DOM and 40% of fluorescence attributed to protein‐like DOM were degraded over the first days of the incubation indicating that protein‐like DOM is likely a labile component of phytoplankton exudates. In contrast, fluorescence measurements suggest that humic‐like substances are resistant to bacterial degradation over the 24 d of the experiment. Despite fluctuations in the short‐term rates of high‐molecular‐weight and low‐molecular‐weight DOM removal, the relative contributions of these fractions to DOM pool were similar in the fresh exudates and at the end of our incubation experiments. [ABSTRACT FROM AUTHOR]

In the oligotrophic ocean where inorganic phosphate (Pi) concentrations are low, microorganisms supplement their nutrient requirements with phosphorus (P) extracted from dissolved organic matter (DOM). Most P in DOM is bound as phosphate esters, which are hydrolyzed by phosphoesterases to Pi. However, a large fraction of DOM‐P occurs as phosphonates, reduced organophosphorus compounds with a CP bond that do not yield Pi through simple ester hydrolysis alone. Phosphonates require an additional step that cleaves the CP bond and oxidizes P(III) to P(V) to yield Pi. Most phosphonates are metabolized by the C‐P lyase pathway, which cleaves CP bonds and oxidizes phosphonates to Pi, enabling microbial assimilation. While the activity of common phosphoesterases such as alkaline phosphatase and phosphodiesterase can be measured by a fluorescent assay, a comparable method to assess C‐P lyase activity (CLA) in natural water samples does not exist. To address this, we synthesized a dansyl‐labeled phosphonate compound, and measured its hydrolysis by C‐P lyase using high performance liquid chromatography. We found that laboratory cultures of marine bacteria expressing the C‐P lyase pathway are able to hydrolyze the dansyl phosphonate, while bacteria expressing other phosphonate degradation pathways do not. Finally, we performed several field tests of the assay to measure water column profiles of CLA at Sta. ALOHA in the North Pacific Subtropical Gyre. Activity was elevated near the deep chlorophyll maximum suggesting high levels of phosphonate degradation in that region. [ABSTRACT FROM AUTHOR]

COMMENTARY Unifyingchemicalandbiologicalperspectivesof carbonaccumulationintheenvironment Daniel J. Repeta a,1  Heterotrophic microorganisms are fiendishly clever at degrading allshapes andsizes oforganiccompounds to extract the energy they need to build biomass. This distribution of DOM has long been recognized to imply strong feedbacks between DOM production and consumption, but the mechanistic underpinnings of those feedbacks have never been described. At the molecular level, the interaction of DOM supply, microbial uptake and respiration, and microbial community dynamics leads to a bimodal distribution of DOM pools. Other G1 DOM1 DOM2 DOM3 G2 G3 G4 S1 S2 G5 High Productivity High Biomass Rapid cycling High DOM Low productivity Low biomass Slower cycling Low DOM Depth DOM Concentration Fig. [Extracted from the article]

Summary: In tropical and subtropical oceanic surface waters phosphate scarcity can limit microbial productivity. However, these environments also have bioavailable forms of phosphorus incorporated into dissolved organic matter (DOM) that microbes with the necessary transport and hydrolysis metabolic pathways can access to supplement their phosphorus requirements. In this study we evaluated how the environment shapes the abundance and taxonomic distribution of the bacterial carbon–phosphorus (C–P) lyase pathway, an enzyme complex evolved to extract phosphate from phosphonates. Phosphonates are organophosphorus compounds characterized by a highly stable C–P bond and are enriched in marine DOM. Similar to other known bacterial adaptions to low phosphate environments, C–P lyase was found to become more prevalent as phosphate concentrations decreased. C–P lyase was particularly enriched in the Mediterranean Sea and North Atlantic Ocean, two regions that feature sustained periods of phosphate depletion. In these regions, C–P lyase was prevalent in several lineages of Alphaproteobacteria (Pelagibacter, SAR116, Roseobacter and Rhodospirillales), Gammaproteobacteria, and Actinobacteria. The global scope of this analysis supports previous studies that infer phosphonate catabolism via C–P lyase is an important adaptive strategy implemented by bacteria to alleviate phosphate limitation and expands the known geographic extent and taxonomic affiliation of this metabolic pathway in the ocean. [ABSTRACT FROM AUTHOR]

Abstract Marine dissolved organic carbon (DOC) is highly depleted in radiocarbon and thus inferred to be largely refractory to removal processes that operate on less than millennial timescales. However, a growing number of reports have shown that a large fraction of marine DOC can be effectively removed during circulation through submarine hydrothermal systems. What is not clear, however, is whether the DOC that remains in hydrothermal fluids is remnant non-reactive DOC from recharged seawater, or DOC that has been largely produced in the subsurface. We collected and characterized warm (∼65 °C) hydrothermal fluids from deep (18, 40, 73, 200 m) within the basalt-hosted basement of the Juan de Fuca Ridge flank in the Northeast Pacific Ocean. DOC concentrations in hydrothermal fluids were 9 to 18 μM, much lower than measured in local deep seawater (37.5 μM). DOC Δ 14 C values of −683‰ to −856‰ were much lower than the Δ 14 C-dissolved inorganic carbon (DIC) values of −880‰ to −918‰, while DOC δ 13 C values of −23.6‰ to −27.0‰ were much heavier than that of the particulate organic carbon (POC) pool (∼ − 34 ‰), suggesting that biological production in the subsurface is not a primary source of DOC. Rather, our data suggest that isotopically enriched DOC are selectively removed from recharged seawater, leaving DOC that is very isotopically depleted in the basaltic basement fluids. Despite the removal of 50–75% of DOC in the subsurface, nuclear magnetic resonance (NMR) functional group analyses indicate that aromatic compounds were added to basaltic basement fluids during passage through the deep subseafloor and may partly contribute to the depleted 14C DOC in the ridge-flank basement fluids. Highlights • Isotopically enriched dissolved organic carbon removed in basaltic basement. • Aromatic carbon is added to fluids during passage through the basaltic subseafloor. • Carbon isotopic data suggest biological production not a primary contributor to DOC. [ABSTRACT FROM AUTHOR]

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., NH415NO3). 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. [ABSTRACT FROM AUTHOR]

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 and that quantification is possible using internal standards (e.g., NH415NO3). Sample volumes of 2-4 uL with total solution concentrations of at least 0.2-g/L form sufficient particle mass for elemental ratio measurement by the AMS, despite only a small fraction (~ 0.1 %) of the sample forming fine particles while the remainder end up as larger droplets. The method was applied to aerosol filter extracts from the field and laboratory, as well as to 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 and atmospheric dissolved organic matter. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract: Dissolved organic matter (DOM) is the largest active organic carbon reservoir in the ocean (662GT 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 (15m) to bathypelagic (1800m) 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 1800m 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. [Copyright &y& Elsevier]

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. [Copyright &y& Elsevier]