Benzoyl Chloride Derivatization Advances the Quantification of Dissolved Polar Metabolites on Coral Reefs

Extracellular chemical cues constitute much of the language of life among marine organisms, from microbes to mammals. Changes in this chemical pool serve as invisible signals of overall ecosystem health and disruption to this finely tuned equilibrium. In coral reefs, the scope and magnitude of the chemicals involved in maintaining reef equilibria are largely unknown. Processes involving small, polar molecules, which form the majority components of labile dissolved organic carbon, are often poorly captured using traditional techniques. We employed chemical derivatization with mass spectrometry-based targeted exometabolomics to quantify polar dissolved phase metabolites on five coral reefs in the U.S. Virgin Islands. We quantified 45 polar exometabolites, demonstrated their spatial variability, and contextualized these findings in terms of geographic and benthic cover differences. By comparing our results to previously published coral reef exometabolomes, we show the novel quantification of 23 metabolites, including central carbon metabolism compounds (e.g., glutamate) and novel metabolites such as homoserine betaine. We highlight the immense potential of chemical derivatization-based exometabolomics for quantifying labile chemical cues on coral reefs and measuring molecular level responses to environmental stressors. Overall, improving our understanding of the composition and dynamics of reef exometabolites is vital for effective ecosystem monitoring and management strategies.

Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics

Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.

Metabolite diversity among representatives of divergent Prochlorococcus ecotypes

IMPORTANCE

Approximately half of the annual carbon fixation on Earth occurs in the surface ocean through the photosynthetic activities of phytoplankton such as the ubiquitous picocyanobacterium Prochlorococcus. Ecologically distinct subpopulations (or ecotypes) of Prochlorococcus are central conduits of organic substrates into the ocean microbiome, thus playing important roles in surface ocean production. We measured the chemical profile of three cultured ecotype strains, observing striking differences among them that have implications for the likely chemical impact of Prochlorococcus subpopulations on their surroundings in the wild. Subpopulations differ in abundance along gradients of temperature, light, and nutrient concentrations, suggesting that these chemical differences could affect carbon cycling in different ocean strata and should be considered in models of Prochlorococcus physiology and marine carbon dynamics.

Microorganisms and dissolved metabolites distinguish Florida's Coral Reef habitats

As coral reef ecosystems experience unprecedented change, effective monitoring of reef features supports management, conservation, and intervention efforts. Omic techniques show promise in quantifying key components of reef ecosystems including dissolved metabolites and microorganisms that may serve as invisible sensors for reef ecosystem dynamics. Dissolved metabolites are released by reef organisms and transferred among microorganisms, acting as chemical currencies and contributing to nutrient cycling and signaling on reefs. Here, we applied four omic techniques (taxonomic microbiome via amplicon sequencing, functional microbiome via shotgun metagenomics, targeted metabolomics, and untargeted metabolomics) to waters overlying Florida's Coral Reef, as well as microbiome profiling on individual coral colonies from these reefs to understand how microbes and dissolved metabolites reflect biogeographical, benthic, and nutrient properties of this 500-km barrier reef. We show that the microbial and metabolite omic approaches each differentiated reef habitats based on geographic zone. Further, seawater microbiome profiling and targeted metabolomics were significantly related to more reef habitat characteristics, such as amount of hard and soft coral, compared to metagenomic sequencing and untargeted metabolomics. Across five coral species, microbiomes were also significantly related to reef zone, followed by species and disease status, suggesting that the geographic water circulation patterns in Florida also impact the microbiomes of reef builders. A combination of differential abundance and indicator species analyses revealed metabolite and microbial signatures of specific reef zones, which demonstrates the utility of these techniques to provide new insights into reef microbial and metabolite features that reflect broader ecosystem processes.

Chitin utilization by marine picocyanobacteria and the evolution of a planktonic lifestyle

Marine picocyanobacteria Prochlorococcus and Synechococcus, the most abundant photosynthetic cells in the oceans, are generally thought to have a primarily single-celled and free-living lifestyle. However, while studying the ability of picocyanobacteria to supplement photosynthetic carbon fixation with the use of exogenous organic carbon, we found the widespread occurrence of genes for breaking down chitin, an abundant source of organic carbon that exists primarily as particles. We show that cells that encode a chitin degradation pathway display chitin degradation activity, attach to chitin particles, and show enhanced growth under low light conditions when exposed to chitosan, a partially deacetylated soluble form of chitin. Marine chitin is largely derived from arthropods, which underwent major diversifications 520 to 535 Mya, close to when marine picocyanobacteria are inferred to have appeared in the ocean. Phylogenetic analyses confirm that the chitin utilization trait was acquired at the root of marine picocyanobacteria. Together this leads us to postulate that attachment to chitin particles allowed benthic cyanobacteria to emulate their mat-based lifestyle in the water column, initiating their expansion into the open ocean, seeding the rise of modern marine ecosystems. Subsequently, transitioning to a constitutive planktonic life without chitin associations led to cellular and genomic streamlining along a major early branch within Prochlorococcus. Our work highlights how the emergence of associations between organisms from different trophic levels, and their coevolution, creates opportunities for colonizing new environments. In this view, the rise of ecological complexity and the expansion of the biosphere are deeply intertwined processes.

Benthic exometabolites and their ecological significance on threatened Caribbean coral reefs

Benthic organisms are the architectural framework supporting coral reef ecosystems, but their community composition has recently shifted on many reefs. Little is known about the metabolites released from these benthic organisms and how compositional shifts may influence other reef life, including prolific microorganisms. To investigate the metabolite composition of benthic exudates and their ecological significance for reef microbial communities, we harvested exudates from six species of Caribbean benthic organisms including stony corals, octocorals, and an invasive encrusting alga, and subjected these exudates to untargeted and targeted metabolomics approaches using liquid chromatography-mass spectrometry. Incubations with reef seawater microorganisms were conducted to monitor changes in microbial abundances and community composition using 16 S rRNA gene sequencing in relation to exudate source and three specific metabolites. Exudates were enriched in amino acids, nucleosides, vitamins, and indole-based metabolites, showing that benthic organisms contribute labile organic matter to reefs. Furthermore, exudate compositions were species-specific, and riboflavin and pantothenic acid emerged as significant coral-produced metabolites, while caffeine emerged as a significant invasive algal-produced metabolite. Microbial abundances and individual microbial taxa responded differently to exudates from stony corals and octocorals, demonstrating that exudate mixtures released from different coral species select for specific bacteria. In contrast, microbial communities did not respond to individual additions of riboflavin, pantothenic acid, or caffeine. This work indicates that recent shifts in benthic organisms alter exudate composition and likely impact microbial communities on coral reefs.

Microbial metabolites in the marine carbon cycle

One-quarter of photosynthesis-derived carbon on Earth rapidly cycles through a set of short-lived seawater metabolites that are generated from the activities of marine phytoplankton, bacteria, grazers and viruses. Here we discuss the sources of microbial metabolites in the surface ocean, their roles in ecology and biogeochemistry, and approaches that can be used to analyse them from chemistry, biology, modelling and data science. Although microbial-derived metabolites account for only a minor fraction of the total reservoir of marine dissolved organic carbon, their flux and fate underpins the central role of the ocean in sustaining life on Earth.

Linkages Among Dissolved Organic Matter Export, Dissolved Metabolites, and Associated Microbial Community Structure Response in the Northwestern Sargasso Sea on a Seasonal Scale

Deep convective mixing of dissolved and suspended organic matter from the surface to depth can represent an important export pathway of the biological carbon pump. The seasonally oligotrophic Sargasso Sea experiences annual winter convective mixing to as deep as 300 m, providing a unique model system to examine dissolved organic matter (DOM) export and its subsequent compositional transformation by microbial oxidation. We analyzed biogeochemical and microbial parameters collected from the northwestern Sargasso Sea, including bulk dissolved organic carbon (DOC), total dissolved amino acids (TDAA), dissolved metabolites, bacterial abundance and production, and bacterial community structure, to assess the fate and compositional transformation of DOM by microbes on a seasonal time-scale in 2016–2017. DOM dynamics at the Bermuda Atlantic Time-series Study site followed a general annual trend of DOC accumulation in the surface during stratified periods followed by downward flux during winter convective mixing. Changes in the amino acid concentrations and compositions provide useful indices of diagenetic alteration of DOM. TDAA concentrations and degradation indices increased in the mesopelagic zone during mixing, indicating the export of a relatively less diagenetically altered (i.e., more labile) DOM. During periods of deep mixing, a unique subset of dissolved metabolites, such as amino acids, vitamins, and benzoic acids, was produced or lost. DOM export and compositional change were accompanied by mesopelagic bacterial growth and response of specific bacterial lineages in the SAR11, SAR202, and SAR86 clades, Acidimicrobiales, and Flavobacteria, during and shortly following deep mixing. Complementary DOM biogeochemistry and microbial measurements revealed seasonal changes in DOM composition and diagenetic state, highlighting microbial alteration of the quantity and quality of DOM in the ocean.

Advances in Chemical Analysis of Oil Spills Since the Deepwater Horizon Disaster

Analytical techniques for chemical analysis of oil, oil photochemical and biological transformation products, and dispersants and their biodegradation products benefited significantly from research following the 2010 Deepwater Horizon (DWH) disaster. Crude oil and weathered-oil matrix reference materials were developed based on the Macondo well oil and characterized for polycyclic aromatic hydrocarbons, hopanes, and steranes for use to assure and improve the quality of analytical measurements in oil spill research. Advanced gas chromatography (GC) techniques such as comprehensive two-dimensional GC (GC × GC), pyrolysis GC with mass spectrometry (MS), and GC with tandem MS (GC-MS/MS) provide a greater understanding at the molecular level of composition and complexity of oil and weathering changes. The capabilities of high-resolution MS (HRMS) were utilized to extend the analytical characterization window beyond conventional GC-based methods to include polar and high molecular mass components (>400 Da) and to provide new opportunities for discovery, characterization, and investigation of photooxidation and biotransformation products. Novel separation approaches to reduce the complexity of the oil and weathered oil prior to high-resolution MS and advanced fluorescence spectrometry have increased the information available on spilled oil and transformation products. HRMS methods were developed to achieve the required precision and sensitivity for detection of dispersants and to provide molecular-level characterization of the complex surfactants. Overall, research funding following the DWH oil spill significantly advanced and expanded the use of analytical techniques for chemical analysis to support petroleum and dispersant characterization and investigations of fate and effects of not only the DWH oil spill but future spills.

Analysis of 39 drugs and metabolites, including 8 glucuronide conjugates, in an upstream wastewater network via HPLC-MS/MS

Pharmaceutical compounds ingested by humans are metabolized and excreted in urine and feces. These metabolites can be quantified in wastewater networks using wastewater-based epidemiology (WBE) methods. Standard WBE methods focus on samples collected at wastewater treatment plants (WWTPs). However, these methods do not capture more labile classes of metabolites such as glucuronide conjugates, products of the major phase II metabolic pathway for drug elimination. By shifting sample collection more upstream, these unambiguous markers of human exposure are captured before hydrolysis in the wastewater network. In this paper, we present an HPLC-MS/MS method that quantifies 8 glucuronide conjugates in addition to 31 parent and other metabolites of prescription and synthetic opioids, overdose treatment drugs, illicit drugs, and population markers. Calibration curves for all analytes are linear (r2 > 0.98), except THC (r2 = 0.97), and in the targeted range (0.1-1,000 ng mL-1) with lower limits of quantification (S/N = 9) ranging from 0.098 to 48.75 ng mL-1. This method is fast with an injection-to-injection time of 7.5 min. We demonstrate the application of the method to five wastewater samples collected from a manhole in a city in eastern Massachusetts. Collected wastewater samples were filtered and extracted via solid-phase extraction (SPE). The SPE cartridges are eluted and concentrated in the laboratory via nitrogen-drying. The method and case study presented here demonstrate the potential and application of expanding WBE to monitoring labile metabolites in upstream wastewater networks.

Quantification of Amine- and Alcohol-Containing Metabolites in Saline Samples Using Pre-extraction Benzoyl Chloride Derivatization and Ultrahigh Performance Liquid Chromatography Tandem Mass Spectrometry (UHPLC MS/MS)

Dissolved metabolites serve as nutrition, energy, and chemical signals for microbial systems. However, the full scope and magnitude of these processes in marine systems are unknown, largely due to insufficient methods, including poor extraction of small, polar compounds using common solid-phase extraction resins. Here, we utilized pre-extraction derivatization and ultrahigh performance liquid chromatography electrospray ionization tandem mass spectrometry (UHPLC-ESI-MS/MS) to detect and quantify targeted dissolved metabolites in seawater and saline culture media. Metabolites were derivatized with benzoyl chloride by their primary and secondary amine and alcohol functionalities and quantified using stable isotope-labeled internal standards (SIL-ISs) produced from ¹³C₆-labeled benzoyl chloride. We optimized derivatization, extraction, and sample preparation for field and culture samples and evaluated matrix-derived biases. We have optimized this quantitative method for 73 common metabolites, of which 50 cannot be quantified without derivatization due to low extraction efficiencies. Of the 73 metabolites, 66 were identified in either culture media or seawater and 45 of those were quantified. This derivatization method is sensitive (detection limits = pM to nM), rapid (∼5 min per sample), and high throughput.

Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy

The communities of bacteria that assemble around marine microphytoplankton are predictably dominated by Rhodobacterales, Flavobacteriales, and families within the Gammaproteobacteria. Yet whether this consistent ecological pattern reflects the result of resource-based niche partitioning or resource competition requires better knowledge of the metabolites linking microbial autotrophs and heterotrophs in the surface ocean. We characterized molecules targeted for uptake by three heterotrophic bacteria individually co-cultured with a marine diatom using two strategies that vetted the exometabolite pool for biological relevance by means of bacterial activity assays: expression of diagnostic genes and net drawdown of exometabolites, the latter detected with mass spectrometry and nuclear magnetic resonance using novel sample preparation approaches. Of the more than 36 organic molecules with evidence of bacterial uptake, 53% contained nitrogen (including nucleosides and amino acids), 11% were organic sulfur compounds (including dihydroxypropanesulfonate and dimethysulfoniopropionate), and 28% were components of polysaccharides (including chrysolaminarin, chitin, and alginate). Overlap in phytoplankton-derived metabolite use by bacteria in the absence of competition was low, and only guanosine, proline, and N-acetyl-D-glucosamine were predicted to be used by all three. Exometabolite uptake pattern points to a key role for ecological resource partitioning in the assembly marine bacterial communities transforming recent photosynthate.

Metabolomics as an Emerging Tool in the Search for Astrobiologically Relevant Biomarkers

It is now routinely possible to sequence and recover microbial genomes from environmental samples. To the degree it is feasible to assign transcriptional and translational functions to these genomes, it should be possible, in principle, to largely understand the complete molecular inputs and outputs of a microbial community. However, gene-based tools alone are presently insufficient to describe the full suite of chemical reactions and small molecules that compose a living cell. Metabolomic tools have developed quickly and now enable rapid detection and identification of small molecules within biological and environmental samples. The convergence of these technologies will soon facilitate the detection of novel enzymatic activities, novel organisms, and potentially extraterrestrial life-forms on solar system bodies. This review explores the methodological problems and scientific opportunities facing researchers who hope to apply metabolomic methods in astrobiology-related fields, and how present challenges might be overcome.

AutoTuner: High Fidelity and Robust Parameter Selection for Metabolomics Data Processing

Untargeted metabolomics experiments provide a snapshot of cellular metabolism but remain challenging to interpret due to the computational complexity involved in data processing and analysis. Prior to any interpretation, raw data must be processed to remove noise and to align mass-spectral peaks across samples. This step requires selection of dataset-specific parameters, as erroneous parameters can result in noise inflation. While several algorithms exist to automate parameter selection, each depends on gradient descent optimization functions. In contrast, our new parameter optimization algorithm, AutoTuner, obtains parameter estimates from raw data in a single step as opposed to many iterations. Here, we tested the accuracy and the run-time of AutoTuner in comparison to isotopologue parameter optimization (IPO), the most commonly used parameter selection tool, and compared the resulting parameters’ influence on the properties of feature tables after processing. We performed a Monte Carlo experiment to test the robustness of AutoTuner parameter selection and found that AutoTuner generated similar parameter estimates from random subsets of samples. We conclude that AutoTuner is a desirable alternative to existing tools, because it is scalable, highly robust, and very fast (∼100–1000× speed improvement from other algorithms going from days to minutes). AutoTuner is freely available as an R package through BioConductor.

Intracellular Metabolites in Marine Microorganisms during an Experiment Evaluating Microbial Mortality

Metabolomics is a tool with immense potential for providing insight into the impact of biological processes on the environment. Here, we used metabolomics methods to characterize intracellular metabolites within marine microorganisms during a manipulation experiment that was designed to test the impact of two sources of microbial mortality, protozoan grazing and viral lysis. Intracellular metabolites were analyzed with targeted and untargeted mass spectrometry methods. The treatment with reduced viral mortality showed the largest changes in metabolite concentrations, although there were organic compounds that shifted when the impact of protozoan grazers was reduced. Intracellular concentrations of guanine, phenylalanine, glutamic acid, and ectoine presented significant responses to changes in the source of mortality. Unexpectedly, variability in metabolite concentrations were not accompanied by increases in microbial abundance which indicates that marine microorganisms altered their internal organic carbon stores without changes in biomass or microbial growth. We used Weighted Correlation Network Analysis (WGCNA) to identify correlations between the targeted and untargeted mass spectrometry data. This analysis revealed multiple unknown organic compounds were correlated with compatible solutes, also called osmolytes or chemical chaperones, which emphasizes the dominant role of compatible solutes in marine microorganisms.

Hepatic metabolite profiling of polychlorinated biphenyl (PCB)-resistant and sensitive populations of Atlantic killifish (Fundulus heteroclitus)

Atlantic killifish inhabiting polluted sites along the east coast of the U.S. have evolved resistance to toxic effects of contaminants. One such contaminated site is the Acushnet River estuary, near New Bedford Harbor (NBH), Massachusetts, which is characterized by very high PCB concentrations in the sediments and in the tissues of resident killifish. Though killifish at this site appear to be thriving, the metabolic costs of survival in a highly contaminated environment are not well understood. In this study we compared the hepatic metabolite profiles of resistant (NBH) and sensitive populations (Scorton Creek (SC), Sandwich, MA) using a targeted metabolomics approach in which polar metabolites were extracted from adult fish livers and quantified. Our results revealed differences in the levels of several metabolites between fish from the two sites. The majority of these metabolites are associated with one-carbon metabolism, an important pathway that supports multiple physiological processes including DNA and protein methylation, nucleic acid biosynthesis and amino acid metabolism. We measured the gene expression of DNA methylation (DNA methyltransferase 1, dnmt1) and demethylation genes (Ten-Eleven Translocation (TET) genes) in the two populations, and observed lower levels of dnmt1 and higher levels of TET gene expression in the NBH livers, suggesting possible differences in DNA methylation profiles. Consistent with this, the two populations differed significantly in the levels of 5-methylcytosine and 5-hydroxymethylcytosine nucleotides. Overall, our results suggest that the unique hepatic metabolite signatures observed in NBH and SC reflect the adaptive mechanisms for survival in their respective habitats.

Discrete Organic Phosphorus Signatures are Evident in Pollutant Sources within a Lake Erie Tributary

Phosphorus loads are strongly associated with the severity of harmful algal blooms in Lake Erie, a Great Lake situated between the United States and Canada. Inorganic and total phosphorus measurements have historically been used to estimate nonpoint and point source contributions, from contributing watersheds with organic phosphorus often neglected. Here, we used ultrahigh resolution mass spectrometry to characterize the dissolved organic matter and specifically dissolved organic phosphorus composition of several nutrient pollutant source materials and aqueous samples in a Lake Erie tributary. We detected between 23 and 313 organic phosphorus formulas across our samples, with manure samples having greater abundance of phosphorus- and nitrogen containing compounds compared to other samples. Manures also were enriched in lipids and protein-like compounds. The greatest similarities were observed between the Sandusky River and wastewater treatment plant effluent (WWTP), or the Sandusky River and agricultural edge of field samples. These sample pairs shared 84% of organic compounds and 59-73% of P-containing organic compounds, respectively. This similarity suggests that agricultural and/or WWTP sources dominate the supply of organic phosphorus compounds to the river. We identify formulas shared between the river and pollutant sources that could serve as possible markers of source contamination in the tributary.

Targeted metabolomics reveals proline as a major osmolyte in the chemolithoautotroph Sulfurimonas denitrificans

Chemoautotrophic bacteria belonging to the genus Sulfurimonas in the class Campylobacteria are widespread in many marine environments characterized by redox interfaces, yet little is known about their physiological adaptations to different environmental conditions. Here, we used liquid chromatography coupled with tandem mass spectrometry (LC‐MS/MS) in a targeted metabolomics approach to study the adaptations of Sulfurimonas denitrificans to varying salt concentrations that are found in its natural habitat of tidal mudflats. Proline was identified as one of the most abundant internal metabolites and its concentration showed a strong positive correlation with ionic strength, suggesting that it acts as an important osmolyte in S. denitrificans. 2,3‐dihydroxypropane‐1‐sulfonate was also positively correlated with ionic strength, indicating it might play a previously unrecognized role in osmoregulation. Furthermore, the detection of metabolites from the reductive tricarboxylic acid cycle at high internal concentrations reinforces the importance of this pathway for carbon fixation in Campylobacteria and as a hub for biosynthesis. As the first report of metabolomic data for an campylobacterial chemolithoautotroph, this study provides data that will be useful to understand the adaptations of Campylobacteria to their natural habitat at redox interfaces.

Sponge exhalent seawater contains a unique chemical profile of dissolved organic matter

Sponges are efficient filter feeders, removing significant portions of particulate and dissolved organic matter (POM, DOM) from the water column. While the assimilation and respiration of POM and DOM by sponges and their abundant microbial symbiont communities have received much attention, there is virtually no information on the impact of sponge holobiont metabolism on the composition of DOM at a molecular-level. We applied untargeted and targeted metabolomics techniques to characterize DOM in seawater samples prior to entering the sponge (inhalant reef water), in samples exiting the sponge (exhalent seawater), and in samples collected just outside the reef area (off reef seawater). Samples were collected from two sponge species, Ircinia campana and Spheciospongia vesparium, on a near-shore hard bottom reef in the Florida Keys. Metabolic profiles generated from untargeted metabolomics analysis indicated that many more compounds were enhanced in the exhalent samples than in the inhalant samples. Targeted metabolomics analysis revealed differences in diversity and concentration of metabolites between exhalent and off reef seawater. For example, most of the nucleosides were enriched in the exhalent seawater, while the aromatic amino acids, caffeine and the nucleoside xanthosine were elevated in the off reef water samples. Although the metabolic profile of the exhalent seawater was unique, the impact of sponge metabolism on the overall reef DOM profile was spatially limited in our study. There were also no significant differences in the metabolic profiles of exhalent water between the two sponge species, potentially indicating that there is a characteristic DOM profile in the exhalent seawater of Caribbean sponges. Additional work is needed to determine whether the impact of sponge DOM is greater in habitats with higher sponge cover and diversity. This work provides the first insight into the molecular-level impact of sponge holobiont metabolism on reef DOM and establishes a foundation for future experimental studies addressing the influence of sponge-derived DOM on chemical and ecological processes in coral reef ecosystems.

Using network analysis to discern compositional patterns in ultrahigh-resolution mass spectrometry data of dissolved organic matter

RATIONALE

Marine dissolved organic matter (DOM) has long been recognized as a large and dynamic component of the global carbon cycle. Yet, DOM is chemically varied and complex and these attributes present challenges to researchers interested in addressing questions about the role of DOM in global biogeochemical cycles.

METHODS

Organic matter extracts from seawater were analyzed by direct infusion with electrospray ionization into a Fourier transform ion cyclotron resonance mass spectrometer. Network analysis was used to quantify the number of chemical transformations between mass-to-charge values in each sample. The network of chemical transformations was calculated using the MetaNetter plug-in within Cytoscape. The chemical transformations serve as markers for the shared structural characteristics of compounds within complex DOM.

RESULTS

Network analysis revealed that transformations involving selected sulfur-containing moieties and isomers of amino acids were more prevalent in the deep sea than in the surface ocean. Common chemical transformations were not significantly different between the deep sea and surface ocean. Network analysis complements existing computational tools used to analyze ultrahigh-resolution mass spectrometry data.

CONCLUSIONS

This combination of ultrahigh-resolution mass spectrometry with novel computational tools has identified new potential building blocks of organic compounds in the deep sea, including the unexpected importance of dissolved organic sulfur components. The method described here can be readily applied by researchers to analyze heterogeneous and complex DOM. Copyright © 2016 John Wiley & Sons, Ltd.

Steroidal estrogen sources in a sewage-impacted coastal ocean

Estrogens are known to be potent endocrine disrupting chemicals that are commonly found in wastewater effluents at ng L(-1) levels. Yet, we know very little about the distribution and fate of estrogens in coastal oceans that receive wastewater inputs. This study measured a wide range of steroidal estrogens in sewage-impacted seawater using ultra high performance liquid chromatography (UHPLC) tandem mass spectrometry (MS/MS) together with the method of standard addition. In Massachusetts Bay, we find conjugated, free, and halogenated estrogens at concentrations that are consistent with dilution at sites close to the sewage source. At a site 6 miles down current of the sewage source, we observe estrone (E1) concentrations (520 ± 180 pg L(-1)) that are nearly double the nearfield concentrations (320 ± 60 pg L(-1)) despite 9-fold dilution of carbamazepine, which was used as a conservative sewage tracer. Our results suggest that background E1 concentrations in Massachusetts Bay (∼270 ± 50 pg L(-1)) are derived largely from sources unrelated to wastewater effluent such as marine vertebrates.

Evidence for quorum sensing and differential metabolite production by a marine bacterium in response to DMSP

Microbes, the foundation of the marine foodweb, do not function in isolation, but rather rely on molecular level interactions among species to thrive. Although certain types of interactions between autotrophic and heterotrophic microorganisms have been well documented, the role of specific organic molecules in regulating inter-species relationships and supporting growth are only beginning to be understood. Here, we examine one such interaction by characterizing the metabolic response of a heterotrophic marine bacterium, Ruegeria pomeroyi DSS-3, to growth on dimethylsulfoniopropionate (DMSP), an abundant organosulfur metabolite produced by phytoplankton. When cultivated on DMSP, R. pomeroyi synthesized a quorum-sensing molecule, N-(3-oxotetradecanoyl)-l-homoserine lactone, at significantly higher levels than during growth on propionate. Concomitant with the production of a quorum-sensing molecule, we observed differential production of intra- and extracellular metabolites including glutamine, vitamin B2 and biosynthetic intermediates of cyclic amino acids. Our metabolomics data indicate that R. pomeroyi changes regulation of its biochemical pathways in a manner that is adaptive for a cooperative lifestyle in the presence of DMSP, in anticipation of phytoplankton-derived nutrients and higher microbial density. This behavior is likely to occur on sinking marine particles, indicating that this response may impact the fate of organic matter.

Chemical Composition and Potential Environmental Impacts of Water-Soluble Polar Crude Oil Components Inferred from ESI FT-ICR MS

Polar petroleum components enter marine environments through oil spills and natural seepages each year. Lately, they are receiving increased attention due to their potential toxicity to marine organisms and persistence in the environment. We conducted a laboratory experiment and employed state-of-the-art Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) to characterize the polar petroleum components within two operationally-defined seawater fractions: the water-soluble fraction (WSF), which includes only water-soluble molecules, and the water-accommodated fraction (WAF), which includes WSF and microscopic oil droplets. Our results show that compounds with higher heteroatom (N, S, O) to carbon ratios (NSO:C) than the parent oil were selectively partitioned into seawater in both fractions, reflecting the influence of polarity on aqueous solubility. WAF and WSF were compositionally distinct, with unique distributions of compounds across a range of hydrophobicity. These compositional differences will likely result in disparate impacts on environmental health and organismal toxicity, and thus highlight the need to distinguish between these often-interchangeable terminologies in toxicology studies. We use an empirical model to estimate hydrophobicity character for individual molecules within these complex mixtures and provide an estimate of the potential environmental impacts of different crude oil components.

Release of ecologically relevant metabolites by the cyanobacterium Synechococcus elongates CCMP 1631

Photoautotrophic plankton in the surface ocean release organic compounds that fuel secondary production by heterotrophic bacteria. Here we show that an abundant marine cyanobacterium, Synechococcus elongatus, contributes a variety of nitrogen-rich and sulfur-containing compounds to dissolved organic matter. A combination of targeted and untargeted metabolomics and genomic tools was used to characterize the intracellular and extracellular metabolites of S. elongatus. Aromatic compounds, such as 4-hydroxybenzoic acid and phenylalanine, as well as nucleosides (e.g. thymidine, 5'-methylthioadenosine, xanthosine), the organosulfur compound 3-mercaptopropionate, and the plant auxin indole 3-acetic acid, were released by S. elongatus at multiple time points during its growth. Further, the amino acid kynurenine was found to accumulate in the media even though it was not present in the predicted metabolome of S. elongatus. This indicates that some metabolites, including those not predicted by an organism's genome, are likely excreted into the environment as waste; however, these molecules may have broader ecological relevance if they are labile to nearby microbes. The compounds described herein provide excellent targets for quantitative analysis in field settings to assess the source and lability of dissolved organic matter in situ.

Protist Community Grazing on Prokaryotic Prey in Deep Ocean Water Masses

Oceanic protist grazing at mesopelagic and bathypelagic depths, and their subsequent effects on trophic links between eukaryotes and prokaryotes, are not well constrained. Recent studies show evidence of higher than expected grazing activity by protists down to mesopelagic depths. This study provides the first exploration of protist grazing in the bathypelagic North Atlantic Deep Water (NADW). Grazing was measured throughout the water column at three stations in the South Atlantic using fluorescently-labeled prey analogues. Grazing in the deep Antarctic Intermediate water (AAIW) and NADW at all three stations removed 3.79% ± 1.72% to 31.14% ± 8.24% of the standing prokaryote stock. These results imply that protist grazing may be a significant source of labile organic carbon at certain meso- and bathypelagic depths.

Continuous summer export of nitrogen-rich organic matter from the Greenland Ice Sheet inferred by ultrahigh resolution mass spectrometry

Runoff from glaciers and ice sheets has been acknowledged as a potential source of bioavailable dissolved organic matter (DOM) to downstream ecosystems. This source may become increasingly significant as glacial melt rates increase in response to future climate change. Recent work has identified significant concentrations of bioavailable carbon and iron in Greenland Ice Sheet (GrIS) runoff. The flux characteristics and export of N-rich DOM are poorly understood. Here, we employed electrospray ionization (ESI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to determine the elemental compositions of DOM molecules in supraglacial water and subglacial runoff from a large GrIS outlet glacier. We provide the first detailed temporal analysis of the molecular composition of DOM exported over a full melt season. We find that DOM pools in supraglacial and subglacial runoff are compositionally diverse and that N-rich material is continuously exported throughout the melt season, as the snowline retreats further inland. Identification of protein-like compounds and a high proportion of N-rich DOM, accounting for 27-41% of the DOM molecules identified by ESI FT-ICR MS, may suggest a microbial provenance and high bioavailability of glacially exported DOM to downstream microbial communities.

Measuring free, conjugated, and halogenated estrogens in secondary treated wastewater effluent

Steroidal estrogens are potent endocrine-disrupting chemicals that enter natural waters through the discharge of treated and raw sewage. Because estrogens are detrimental to aquatic organisms at sub-nanogram per liter concentrations, many studies have measured so-called "free" estrogen concentrations in wastewater effluents, rivers, and lakes. Other forms of estrogens are also of potential concern because conjugated estrogens can be easily converted to potent free estrogens by bacteria in wastewater treatment plants and receiving waters and halogenated estrogens are likely produced during wastewater disinfection. However, to the best of our knowledge, no studies have concurrently characterized free, conjugated, and halogenated estrogens. We have developed a method that is capable of simultaneously quantifying free, conjugated, and halogenated estrogens in treated wastewater effluent, in which detection limits were 0.13-1.3 ng L(-1) (free), 0.11-1.0 ng L(-1) (conjugated), and 0.18-18 ng L(-1) (halogenated). An aqueous phase additive, ammonium fluoride, was used to increase the electrospray (negative mode) ionization efficiency of free and halogenated estrogens by factors of 20 and 2.6, respectively. The method was validated using treated effluent from the greater Boston metropolitan area, where conjugated and halogenated estrogens made up 60-70% of the steroidal estrogen load on a molar basis.

Molecular signature of organic nitrogen in septic-impacted groundwater

Dissolved inorganic and organic nitrogen levels are elevated in aquatic systems due to anthropogenic activities. Dissolved organic nitrogen (DON) arises from various sources, and its impact could be more clearly constrained if specific sources were identified and if the molecular-level composition of DON were better understood. In this work, the pharmaceutical carbamazepine was used to identify septic-impacted groundwater in a coastal watershed. Using ultrahigh resolution mass spectrometry data, the nitrogen-containing features of the dissolved organic matter in septic-impacted and non-impacted samples were compared. The septic-impacted groundwater samples have a larger abundance of nitrogen-containing formulas. Impacted samples have additional DON features in the regions ascribed as 'protein-like' and 'lipid-like' in van Krevelen space and have more intense nitrogen-containing features in a specific region of a carbon versus mass plot. These features are potential indicators of dissolved organic nitrogen arising from septic effluents, and this work suggests that ultrahigh resolution mass spectrometry is a valuable tool to identify and characterize sources of DON.

Fate of dispersants associated with the deepwater horizon oil spill

Response actions to the Deepwater Horizon oil spill included the injection of ∼771,000 gallons (2,900,000 L) of chemical dispersant into the flow of oil near the seafloor. Prior to this incident, no deepwater applications of dispersant had been conducted, and thus no data exist on the environmental fate of dispersants in deepwater. We used ultrahigh resolution mass spectrometry and liquid chromatography with tandem mass spectrometry (LC/MS/MS) to identify and quantify one key ingredient of the dispersant, the anionic surfactant DOSS (dioctyl sodium sulfosuccinate), in the Gulf of Mexico deepwater during active flow and again after flow had ceased. Here we show that DOSS was sequestered in deepwater hydrocarbon plumes at 1000-1200 m water depth and did not intermingle with surface dispersant applications. Further, its concentration distribution was consistent with conservative transport and dilution at depth and it persisted up to 300 km from the well, 64 days after deepwater dispersant applications ceased. We conclude that DOSS was selectively associated with the oil and gas phases in the deepwater plume, yet underwent negligible, or slow, rates of biodegradation in the affected waters. These results provide important constraints on accurate modeling of the deepwater plume and critical geochemical contexts for future toxicological studies.

The impact of microbial metabolism on marine dissolved organic matter

Microbes mediate global biogeochemical cycles through their metabolism, and all metabolic processes begin with the interaction between the microbial cell wall or membrane and the external environment. For all heterotrophs and many autotrophs, critical growth substrates and factors are present within the dilute and heterogeneous mixture of compounds that constitutes dissolved organic matter (DOM). In short, the microbe-molecule interaction is one of the fundamental reactions within the global carbon cycle. Here, I summarize recent findings from studies that examine DOM-microbe interactions from either the DOM perspective (organic geochemistry) or the microbe perspective (microbial ecology). Gaps in our knowledge are highlighted and future integrative research directions are proposed.

Automated Analysis of Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectra of Natural Organic Matter

The advent of ultra-high-resolution mass spectrometry has revolutionized the ability of aquatic biogeochemists to examine molecular-level components of complex mixtures of organic matter. The ability to accurately assess the chemical composition, elemental formulas, or both of detected compounds is critical to these studies. Here we build on previous work that uses functional group relationships between compounds to extend elemental formulas of low molecular weight compounds to those of higher molecular weight. We propose an automated compound identification algorithm (CIA) for the analysis of ultra-high-resolution mass spectra of natural organic matter acquired by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. This approach is benchmarked with synthetic data sets of compounds cited in the literature. The sensitivity of our results is examined for different sources of error, and CIA is applied to two previously published data sets. We find that CIA works well for data sets with high mass accuracy (<1 ppm) and can accurately determine the elemental formulas for >95% of all compounds composed of C, H, O, and N. Data with lower mass accuracy must be accompanied with additional knowledge of chemical structure, composition, or both in order to yield accurate elemental formulas.

Identification of black carbon derived structures in a volcanic ash soil humic acid by Fourier transform ion cyclotron resonance mass spectrometry

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), coupled with cross-polarization magic angle spinning 13C nuclear magnetic resonance (NMR) spectroscopy and Kendrick mass defect analysis, was used to study the molecular composition of an aromatic carbon-rich humic acid extracted from a dark black soil from Iwata, Japan. Black carbon, produced by the incomplete combustion of fossil fuels and organic matter, has been suggested as a major component of humic acids having intense peaks in the aromatic and carboxyl regions of the 13C NMR spectrum. Taking advantage of the high resolving power of FT-ICR MS to make precise formula assignments, three different types of highly carboxylated polycyclic aromatic compounds were identified in the sample: linearly fused aromatic structures, aromatic structures linked by carbon-carbon single bonds, and highly condensed aromatic structures. These carboxylated aromatic structures have a low mass defect in their mass spectra due to their abundance of oxygen and deficiency of hydrogen. This mass defect is observed in the vast majority of peaks present in the entire mass spectrum, differentiating them from structures that are hydrogen-rich (e.g., fatty acids, proteins, carbohydrates). Thus, we conclude that the bulk of the sample analyzed is comprised of these heavily carboxylated, hydrogen-deficient, condensed aromatic structures, features believed to be characteristic of black carbon-like material.

High-resolution Fourier transform ion cyclotron resonance mass spectrometry of humic and fulvic acids: improvements and comparisons

Full structural characterization of complex mixtures such as humic acid extracts has been elusive because of insufficient compound resolution with conventional techniques. Using electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry, we were able to resolve individual compounds within humic and fulvic acid mixtures (mass resolving power approximately 80000 at 300 m/z). We examined two samples in detail: (1) dissolved organic matter (primarily fulvic acids) from Suwannee River, GA, and (2) a humic acid extract from a degraded wood collected on Mt. Rainier, WA. Sample conditions (such as solvent, pH, and concentration) and instrument parameters (such as source voltages, trapping potentials, and excitation parameters) were optimized to yield the highest mass resolving power with the least mass discrimination in positive ion mode. High resolving power was achieved with low ion densities combined with coadding numerous scans. The increased resolution allowed molecular-level comparisons of the two samples which in turn could be used to estimate the relative similarity of individual compound distribution as well as an indication of the dominant diagenetic processes in the two source environments.

Marine protozoa produce organic matter with a high affinity for PCBs during grazing

Processes influencing organic carbon distribution and composition can control the speciation of organic contaminants such as polychlorinated biphenyls (PCBs) and ultimately determine their residence time in aquatic environments. Protozoan grazers are active in the remineralization and recycling of organic material both in the water column and at the sediment-water interface. Thus, they influence the quality and quantity of potential PCB binding substrates in the suspended and dissolved phases of aqueous systems. In this study, common headspace systems were used to compare the chlorobiphenyl-binding affinity of dissolved organic carbon (DOC) in protozoan and bacterial culture filtrates (<0.2 microm) relative to DOC in a seawater control. Culture filtrates from three marine protozoan species were compared-Uronema sp., Cafeteria sp., and Paraphysomonas imperforata. Each protozoan species was fed the same bacterial prey, Halomonas halodurans, which was also used as a bacterial control. Affinities of culture DOC for [14C]3,3',4,4'-tetrachlorobiphenyl (IUPAC 77) were normalized to DOC and surfactant concentrations. Values of DOC equilibrium partition coefficients (K(DOC)) ranged from 10(4.6) in seawater (Vineyard Sound, MA) to 10(5.4) and 10(5.5) in protist cultures, indicating that grazer-modified DOC was a better sorbent for PCBs than DOC in bacterial or seawater controls.

Importance of passive diffusion in the uptake of polychlorinated biphenyls by phagotrophic protozoa

Unicellular protozoan grazers represent a size class of organisms where a transition in the mechanism of chlorobiphenyl (CB) introduction, from diffusion through surface membranes to ingestion of contaminated prey, could occur. This study compares the relative importance of these two processes in the overall uptake of polychlorinated biphenyls by protists. Uptake rates and steady-state concentrations were compared in laboratory cultures of grazing and nongrazing protozoa. These experiments were conducted with a 10-microm marine scuticociliate (Uronema sp.), bacterial prey (Halomonas halodurans), and a suite of 21 CB congeners spanning a range of aqueous solubilities. The dominant pathway of CB uptake by both grazing and nongrazing protozoa was diffusion. Organic-carbon-normalized CB concentrations (in the protozoan cell) were equivalent in grazing and nongrazing protozoa for all congeners studied. Rate constants for uptake into and loss from the protozoan cell were independently determined by using [3,3',4, 4'-(14)C]tetrachlorobiphenyl (IUPAC no. 77), 0.38 +/- 0.03 min(-1) and (1.1 +/- 0.1) x 10(-5) (g of organic carbon)(-1) min(-1), respectively. Magnitudes of the uptake and loss processes were calculated and compared by using a numerical model. The model result was consistent with data from the bioaccumulation experiment and supported the hypothesis that diffusive uptake is faster than ingestive uptake in phagotrophic unicellular protozoa.