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Exudates by the diatom Phaeodactylum tricornutumwere 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.

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 CH4and C2H4in 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 CH4and C2H4, respectively, were readily degraded in proportions consistent with their abundance and bioavailability in HMWDOM and with the concentrations of CH4and C2H4in the water column. We conclude that phosphonate degradation through the C‐P lyase pathway is an important source and a common production pathway of CH4and C2H4in 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.

Coastal upwelling of nutrients and metals along eastern boundary currents fuels some of the most biologically productive marine ecosystems. Although iron is a main driver of productivity in many of these regions, iron cycling and acquisition by microbes remain poorly constrained, in part due to the unknown composition of organic ligands that keep bioavailable iron in solution. In this study, we investigated organic ligand composition in discrete water samples collected across the highly productive California Coastal upwelling system. Siderophores were observed in distinct nutrient regimes at concentrations ranging from 1 pM to 18 pM. Near the shallow continental shelf, ferrioxamine B was observed in recently upwelled, high chlorophyll surface waters while synechobactins were identified within nepheloid layers at 60–90 m depth. In offshore waters characterized by intermediate chlorophyll, iron, and nitrate concentrations, we found amphibactins and an unknown siderophore with a molecular formula of C33H58O8N5Fe. Highest concentrations were measured in the photic zone, however, amphibactins were also found in waters as deep as 1500 m. The distribution of siderophores provides evidence for microbial iron deficiency across a range of nutrient regimes and indicates siderophore production and acquisition is an important strategy for biological iron uptake in iron limited coastal systems. Polydisperse humic ligands were also detected throughout the water column and were particularly abundant near the benthic boundary. Our results highlight the fine‐scale spatial heterogeneity of metal ligand composition in an upwelling environment and elucidate distinct sources that include biological production and the degradation of organic matter in suboxic waters.

We present concentration and isotopic profiles of total, size, and polarity fractionated dissolved organic carbon (DOC) from Station ALOHA (A Long‐term Oligotrophic Habitat Assessment), an oligotrophic site in the North Pacific Ocean. The data show that, between the surface and 3500 m, low molecular weight (LMW) hydrophilic DOC, LMW hydrophobic DOC, and high molecular weight (HMW) DOC constitute 22–33%, 45–52%, and 23–35% of DOC, respectively. LMW hydrophilic DOC is more isotopically depleted (δ13C of −23.9‰ to −31.5‰ and Δ14C of −304‰ to −795‰; mean age of 2850 to 15000 years) than the LMW hydrophobic DOC (δ13C of −22‰ to −23‰ and Δ14C of −270‰ to −568‰; 2470 to 6680 years) and HMW DOC (δ13C of ~−21‰ and Δ14C of −24‰ to −294‰; 135–2700 years). Our analyses suggest that a large fraction of DOC may be derived from allochthonous sources such as terrestrial and hydrothermal DOC and cycle on much longer time scales of >10000 years or enter the ocean as preaged carbon. Different DOC fractions have different radio and stable carbon isotope valuesLarge (~25%) fraction of DOC is highly depleted in both 13C and 14C and may be derived from allochthonous sources13C‐ and 14C‐isotopic enrichments in DOC follow the series: HMW DOC > LMW hydrophobic DOC > LMW hydrophilic DOC

Biogenic methane is widely thought to be a product of archaeal methanogenesis, an anaerobic process that is inhibited or outcompeted by the presence of oxygen and sulfate. Yet a large fraction of marine methane delivered to the atmosphere is produced in high-sulfate, fully oxygenated surface waters that have methane concentrations above atmospheric equilibrium values, an unexplained phenomenon referred to as the marine methane paradox. Here we use nuclear magnetic resonance spectroscopy to show that polysaccharide esters of three phosphonic acids are important constituents of dissolved organic matter in seawater from the North Pacific. In seawater and pure culture incubations, bacterial degradation of these dissolved organic matter phosphonates in the presence of oxygen releases methane, ethylene and propylene gas. Moreover, we found that in mutants of a methane-producing marine bacterium, Pseudomonas stutzeri, disrupted in the C–P lyase phosphonate degradation pathway, methanogenesis was also disabled, indicating that the C–P lyase pathway can catalyse methane production from marine dissolved organic matter. Finally, the carbon stable isotope ratio of methane emitted during our incubations agrees well with anomalous isotopic characteristics of seawater methane. We estimate that daily cycling of only about 0.25% of the organic matter phosphonate inventory would support the entire atmospheric methane flux at our study site. We conclude that aerobic bacterial degradation of phosphonate esters in dissolved organic matter may explain the marine methane paradox.

Current understanding of dissolved iron (Fe) speciation in the ocean is based on two fundamentally different approaches: electrochemical methods that measure bulk properties of a heterogeneous ligand pool and liquid chromatography mass spectrometry methods that characterize ligands at a molecular level. Here, we describe a method for simultaneously determining Fe–ligand dissociation rate constants (kd) of suites of naturally occurring ligands in seawater by monitoring the exchange of ligand-bound 56Fe with 57Fe using liquid chromatography–inductively coupled mass spectrometry. Values of kdwere determined for solutions of ferrichrome and ferrioxamine E. In seawater, the dissociation rate constant of ferrichrome (kd= 10 × 10–8s–1) was greater than that of ferrioxamine E (kd= 3.6 × 10–8s–1). The rates for both compounds were over twice as fast in seawater compared with pure water, suggesting that seawater salts accelerate dissociation. Isotope exchange experiments on organic extracts of natural seawater indicated that ligand-binding sites associated with chromatographically unresolved dissolved organic matter exchanged Fe more quickly (kd= 1.8 × 10–5s–1) than amphibactin siderophores (kd= 2.15 × 10–6s–1) and an unidentified siderophore with m/z709 (kd= 9.6 × 10–6s–1). These findings demonstrate that our approach can bridge molecular-level ligand identification with kinetic and thermodynamic metal-binding properties.

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. Both cyclonic and anticyclonic eddies add iron to the lower euphotic zone of oligotrophic gyresIn an anticyclonic eddy, dissolved iron at the deep chlorophyll maximum increased but productivity did notUptake of upwelled iron and nitrate in a cyclonic eddy led to low iron conditions and stress, but did not limit productivity Both cyclonic and anticyclonic eddies add iron to the lower euphotic zone of oligotrophic gyres In an anticyclonic eddy, dissolved iron at the deep chlorophyll maximum increased but productivity did not Uptake of upwelled iron and nitrate in a cyclonic eddy led to low iron conditions and stress, but did not limit productivity

Rapidly sinking large particles contribute a major portion of the mass flux from marine surface waters to the sea floor. The recognition that organic matter associated with these particles undergoes major alterations in its chemical composition during vertical transit has raised new questions on the role of rapid transformation processes in carbon and nitrogen cycling, benthic nutrition, and post-depositional degradation1. Analysis of specific organic compounds has established some of the compositional changes of these transformations2–4. However, most of the changes observed represent the sum of biological production and degradation. For example, bacterial and chemical degradation of fatty acids in the water column may be completely masked by an even greater production of these compounds by zooplankton. Hence it is often difficult to distinguish between competing degradative processes, and to assess the relative significance of each. Carotenoid pigments have characteristics which make them particularly suitable for use as organic tracers to distinguish between short-term degradation processes. Carotenoids are widely distributed in both photosynthetic and nonphotosynthetic organisms; many of them are source specific; they contain diverse functional groups; and they represent one of the more labile biogenic compound classes in the sea. We report here for the first time the isolation and identification of carotenoid transformation products from sediment trap experiments conducted in coastal marine waters, and discuss the source and significance of observed transformation products with respect to a proposed degradation pathway.

Dissolved organic carbon (DOC) in sea water from Georges Bank was measured by a high temperature combustion/direct injection (HTC/DI) technique during the spring bloom period in April 1993. Concentrations in surface waters (72–85 μM) and deep waters (54–56 μM) were similar to DOC concentrations measured in the oligotrophic north-west Atlantic Ocean by a number of other investigators by various techniques. Although surface values for Chl-a concentrations ranged from 2 to 5 μg l−1, NO3− ranged from 3 to 9 μM and particulate organic carbon (POC) concentrations ranged from 1.0 to 10μM, DOC concentrations only varied by <18‰ DOC was slightly higher (∼5 μM) in the highly productive central bank region than in surrounding stratified surface waters. Relatively constant stable carbon isotopes (DO13C = −22.0 ± 0.5 could not be used to identify a source for these small variations. Slight decreases of DOC (5–12μM) and dissolved organic nitrogen (DON) (0.5–1.0 μM) in filtered sea water kept in the dark was observed over six months, suggesting the presence of a small, labile pool of dissolved organic matter in addition to a large, more refractory reservoir of DOC (∼70 μM) during the spring bloom period on Georges Bank.

ABSTRACTThe members of the OM43 clade of Betaproteobacteriaare abundant coastal methylotrophs with a range of carbon-utilizing capabilities. However, their underlying transcriptional and metabolic responses to shifting conditions or different carbon substrates remain poorly understood. We examined the transcriptional dynamics of OM43 isolate NB0046 subjected to various inorganic nutrient, vitamin, and carbon substrate regimes over different growth phases to (i) develop a quantitative model of its mRNA content; (ii) identify transcriptional markers of physiological activity, nutritional state, and carbon and energy utilization; and (iii) identify pathways involved in methanol or naturally occurring dissolved organic matter (DOM) metabolism. Quantitative transcriptomics, achieved through addition of internal RNA standards, allowed for analyses on a transcripts-per-cell scale. This streamlined bacterium exhibited substantial shifts in total mRNA content (ranging from 1,800 to 17 transcripts cell−1in the exponential and deep stationary phases, respectively) and gene-specific transcript abundances (>1,000-fold increases in some cases), depending on the growth phase and nutrient conditions. Carbon metabolism genes exhibited substantial dynamics, including those for ribulose monophosphate, tricarboxylic acid (TCA), and proteorhodopsin, as well as methanol dehydrogenase (xoxF), which, while always the most abundant transcript, increased from 5 to 120 transcripts cell−1when cultures were nutrient and vitamin amended. In the DOM treatment, upregulation of TCA cycle, methylcitrate cycle, vitamin, and organic phosphorus genes suggested a metabolic route for this complex mixture of carbon substrates. The genome-wide inventory of transcript abundances produced here provides insight into a streamlined marine bacterium’s regulation of carbon metabolism and energy flow, providing benchmarks for evaluating the activity of OM43 populations in situ.IMPORTANCEBacteria exert a substantial influence on marine organic matter flux, yet the carbon components targeted by specific bacterial groups, as well as how those groups’ metabolic activities change under different conditions, are not well understood. Gene expression studies of model organisms can identify these responses under defined conditions, which can then be compared to environmental transcriptomes to elucidate in situactivities. This integration, however, is limited by the data’s relative nature. Here, we report the fully quantitative transcriptome of a marine bacterium, providing a genome-wide survey of cellular transcript abundances and how they change with different states of growth, nutrient conditions, and carbon substrates. The results revealed the dynamic metabolic strategies this methylotroph has for processing both simple one-carbon compounds and the complex multicarbon substrates of naturally derived marine organic matter and provide baseline quantitative data for identifying their in situactivities and impact on the marine carbon cycle.