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The use of ultrafiltration to isolate high molecular weight dissolved organic matter (HMWDOM) from seawater is a fundamental tool in the environmental organic chemist's toolbox. Yet, important characteristics of HMWDOM relevant to its origin and cycling, such as its molecular weight distribution, remain poorly defined. We used diffusion-ordered NMR spectroscopy coupled with mixed-mode chromatography to separate and characterize two major components of marine HMWDOM: acylpolysaccharides (APS) and high molecular weight humic substances (HS). The molecular weights (MWs) of APS and HS both fell within distinct, narrow envelopes; 2.0-16 kDa for APS and 0.9-6.5 kDa for HS. In water samples from the North Pacific Ocean the average MW of both components decreased with depth through the mesopelagic. However, the minimum MW of APS was >2 kDa, well above the molecular weight cutoff of the ultrafilter, suggesting APS removal processes below 2 kDa are highly efficient. The MW distribution of APS shows only small variations with depth, while the MW distribution of HS narrowed due to removal of HMW components. Despite the narrowing of the MW distribution, the concentration of HS did not decrease with depth between 15 and 915 m. This suggests that HMW HS produced in surface waters was either degraded into lower MW compounds without significant remineralization, or that HMW HS was remineralized but replaced by an additional source of HS in the mesopelagic ocean. Based on these results, we propose potential pathways for the production and removal of these major components of HMWDOM.

We have isolated a chlorophyll- d -containing cyanobacterium from the intertidal field site at Moss Beach, on the coast of Central California, USA, where Manning and Strain (1943) originally discovered this far-red chlorophyll. Here, we present the cyanobacterium's environmental description, culturing procedure, pigment composition, ultrastructure, and full genome sequence. Among cultures of far-red cyanobacteria obtained from red algae from the same site, this strain was an epiphyte on a brown macroalgae. Its Q y in vivo absorbance peak is centered at 704-705 nm, the shortest wavelength observed thus far among the various known Acaryochloris strains. Its Chl a /Chl d ratio was 0.01, with Chl d accounting for 99% of the total Chl d and Chl a mass. TEM imagery indicates the absence of phycobilisomes, corroborated by both pigment spectra and genome analysis. The Moss Beach strain codes for only a single set of genes for producing allophycocyanin. Genomic sequencing yielded a 7.25 Mbp circular chromosome and 10 circular plasmids ranging from 16 kbp to 394 kbp. We have determined that this strain shares high similarity with strain S15, an epiphyte of red algae, while its distinct gene complement and ecological niche suggest that this strain could be the closest known relative to the original Chl d source of Manning and Strain (1943). The Moss Beach strain is designated Acaryochloris sp. ( marina ) strain Moss Beach.

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 ( k d ) of suites of naturally occurring ligands in seawater by monitoring the exchange of ligand-bound 56 Fe with 57 Fe using liquid chromatography-inductively coupled mass spectrometry. Values of k d were determined for solutions of ferrichrome and ferrioxamine E. In seawater, the dissociation rate constant of ferrichrome ( k d = 10 × 10 -8 s -1 ) was greater than that of ferrioxamine E ( k d = 3.6 × 10 -8 s -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 ( k d = 1.8 × 10 -5 s -1 ) than amphibactin siderophores ( k d = 2.15 × 10 -6 s -1 ) and an unidentified siderophore with m/z 709 ( k d = 9.6 × 10 -6 s -1 ). These findings demonstrate that our approach can bridge molecular-level ligand identification with kinetic and thermodynamic metal-binding properties.

SignificancePhosphonates are a class of phosphorus metabolites characterized by a highly stable C-P bond. Phosphonates accumulate to high concentrations in seawater, fuel a large fraction of marine methane production, and serve as a source of phosphorus to microbes inhabiting nutrient-limited regions of the oligotrophic ocean. Here, we show that 15% of all bacterioplankton in the surface ocean have genes phosphonate synthesis and that most belong to the abundant groups Prochlorococcus and SAR11. Genomic and chemical evidence suggests that phosphonates are incorporated into cell-surface phosphonoglycoproteins that may act to mitigate cell mortality by grazing and viral lysis. These results underscore the large global biogeochemical impact of relatively rare but highly expressed traits in numerically abundant groups of marine bacteria.

Competing Interests: The author declares no competing interest.

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., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2020 The Authors. Published by Elsevier B.V.)

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., (Copyright © 2019 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

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., (© 2019 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.)

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.

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.

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.

Nearly all iron dissolved in the ocean is complexed by strong organic ligands of unknown composition. The effect of ligand composition on microbial iron acquisition is poorly understood, but amendment experiments using model ligands show they can facilitate or impede iron uptake depending on their identity. Here we show that siderophores, organic compounds synthesized by microbes to facilitate iron uptake, are a dynamic component of the marine ligand pool in the eastern tropical Pacific Ocean. Siderophore concentrations in iron-deficient waters averaged 9 pM, up to fivefold higher than in iron-rich coastal and nutrient-depleted oligotrophic waters, and were dominated by amphibactins, amphiphilic siderophores with cell membrane affinity. Phylogenetic analysis of amphibactin biosynthetic genes suggests that the ability to produce amphibactins has transferred horizontally across multiple Gammaproteobacteria, potentially driven by pressures to compete for iron. In coastal and oligotrophic regions of the eastern Pacific Ocean, amphibactins were replaced with lower concentrations (1-2 pM) of hydrophilic ferrioxamine siderophores. Our results suggest that organic ligand composition changes across the surface ocean in response to environmental pressures. Hydrophilic siderophores are predominantly found across regions of the ocean where iron is not expected to be the limiting nutrient for the microbial community at large. However, in regions with intense competition for iron, some microbes optimize iron acquisition by producing siderophores that minimize diffusive losses to the environment. These siderophores affect iron bioavailability and thus may be an important component of the marine iron cycle., Competing Interests: The authors declare no conflict of interest.

The members of the OM43 clade of Betaproteobacteria are 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 -1 in 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 -1 when 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 IMPORTANCE: Bacteria 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 situ activities. 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 situ activities and impact on the marine carbon cycle., (Copyright © 2016 Gifford et al.)

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.

The role of bacterioplankton in the cycling of marine dissolved organic matter (DOM) is central to the carbon and energy balance in the ocean, yet there are few model organisms available to investigate the genes, metabolic pathways, and biochemical mechanisms involved in the degradation of this globally important carbon pool. To obtain microbial isolates capable of degrading semi-labile DOM for growth, we conducted dilution to extinction cultivation experiments using seawater enriched with high molecular weight (HMW) DOM. In total, 93 isolates were obtained. Amendments using HMW DOM to increase the dissolved organic carbon concentration 4x (280 μM) or 10x (700 μM) the ocean surface water concentrations yielded positive growth in 4-6% of replicate dilutions, whereas <1% scored positive for growth in non-DOM-amended controls. The majority (71%) of isolates displayed a distinct increase in cell yields when grown in increasing concentrations of HMW DOM. Whole-genome sequencing was used to screen the culture collection for purity and to determine the phylogenetic identity of the isolates. Eleven percent of the isolates belonged to the gammaproteobacteria including Alteromonadales (the SAR92 clade) and Vibrio. Surprisingly, 85% of isolates belonged to the methylotrophic OM43 clade of betaproteobacteria, bacteria thought to metabolically specialize in degrading C1 compounds. Growth of these isolates on methanol confirmed their methylotrophic phenotype. Our results indicate that dilution to extinction cultivation enriched with natural sources of organic substrates has a potential to reveal the previously unsuspected relationships between naturally occurring organic nutrients and the microorganisms that consume them.

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 (586 m/z), and C (558 m/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.

Marine dissolved organic carbon (DOC) is a large (660 Pg C) reactive carbon reservoir that mediates the oceanic microbial food web and interacts with climate on both short and long timescales. Carbon isotopic content provides information on the DOC source via δ(13)C and age via Δ(14)C. Bulk isotope measurements suggest a microbially sourced DOC reservoir with two distinct components of differing radiocarbon age. However, such measurements cannot determine internal dynamics and fluxes. Here we analyze serial oxidation experiments to quantify the isotopic diversity of DOC at an oligotrophic site in the central Pacific Ocean. Our results show diversity in both stable and radio isotopes at all depths, confirming DOC cycling hidden within bulk analyses. We confirm the presence of isotopically enriched, modern DOC cocycling with an isotopically depleted older fraction in the upper ocean. However, our results show that up to 30% of the deep DOC reservoir is modern and supported by a 1 Pg/y carbon flux, which is 10 times higher than inferred from bulk isotope measurements. Isotopically depleted material turns over at an apparent time scale of 30,000 y, which is far slower than indicated by bulk isotope measurements. These results are consistent with global DOC measurements and explain both the fluctuations in deep DOC concentration and the anomalous radiocarbon values of DOC in the Southern Ocean. Collectively these results provide an unprecedented view of the ways in which DOC moves through the marine carbon cycle.

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., (© 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Production of dissolved organic matter (DOM) by marine phytoplankton supplies the majority of organic substrate consumed by heterotrophic bacterioplankton in the sea. This production and subsequent consumption converts a vast quantity of carbon, nitrogen, and phosphorus between organic and inorganic forms, directly impacting global cycles of these biologically important elements. Details regarding the chemical composition of DOM produced by marine phytoplankton are sparse, and while often assumed, it is not currently known if phylogenetically distinct groups of marine phytoplankton release characteristic suites of DOM. To investigate the relationship between specific phytoplankton groups and the DOM they release, hydrophobic phytoplankton-derived dissolved organic matter (DOMP) from eight axenic strains was analyzed using high-performance liquid chromatography coupled to mass spectrometry (HPLC-MS). Identification of DOM features derived from Prochlorococcus, Synechococcus, Thalassiosira, and Phaeodactylum revealed DOMP to be complex and highly strain dependent. Connections between DOMP features and the phylogenetic relatedness of these strains were identified on multiple levels of phylogenetic distance, suggesting that marine phytoplankton produce DOM that in part reflects its phylogenetic origin. Chemical information regarding the size and polarity ranges of features from defined biological sources was also obtained. Our findings reveal DOMP composition to be partially conserved among related phytoplankton species, and implicate marine DOM as a potential factor influencing microbial diversity in the sea by acting as a link between autotrophic and heterotrophic microbial community structures.

Organic ligands dominate the speciation of iron in the ocean. Little is known, however, about the chemical composition and distribution of these compounds. Here, we describe a method to detect low concentrations of organic Fe ligands using reverse-phase high-performance liquid chromatography (HPLC) tandem multicollector inductively coupled plasma mass spectrometry. This technique can be used to screen seawater and marine cultures for target compounds that can be isolated and structurally characterized. Sensitive detection (<1 picomole Fe) is achieved using an iron-free HPLC system to reduce background Fe levels, minimizing (40)Ar(16)O(+) interferences on (56)Fe with a hexapole collision cell, and introducing oxygen into the sample carrier gas to prevent the formation of reduced carbon deposits that decrease sensitivity. This method was tested with a chromatographic separation of five trace metal complexes that represent the polarity range likely found in seawater. Good separation was achieved with a 20 min water/methanol gradient, although sensitivity decreased by a factor of 2 at high organic solvent concentrations. Finally, Fe ligand complexes were detected from the organic extract of surface South Pacific seawater and from culture media of the siderophore producing cyanobacteria Synechococcus sp. PCC 7002.

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.

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.

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.

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.