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The exchange of metabolites mediates algal and bacterial interactions that maintain ecosystem function. Yet, while 1000s of metabolites are produced, only a few molecules have been identifiedin these associations. Using the ubiquitous microalgae Pseudo-nitzschia sp., as a model, we employed an untargeted metabolomics strategy to assign structural characteristics to themetabolites that distinguished specific diatom-microbiome associations. We cultured five species of Pseudo-nitzschia, including two species that produced the toxin domoic acid, and examinedtheir microbiomes and metabolomes. A total of 4826 molecular features were detected by tandem mass spectrometry. Only 229 of these could be annotated using available mass spectral libraries,but by applying new in-silico annotation tools, characterization was expanded to 2710 features. The metabolomes of the Pseudo-nitzschia-microbiome associations were distinct and distinguished by structurally diverse nitrogen compounds, ranging from simple amines andamides to cyclic compounds such as imidazoles, pyrrolidines, and lactams. By illuminating the dark metabolomes, this study expands our capacity to discover new chemical targets that facilitatemicrobial partnerships and uncovers the chemical diversity that underpins algae-bacteria interactions.

Although metals are essential for the molecular machineries of life, systematic methods for discovering metal-small molecule complexes from biological samples are limited. Here, we describe a two-step native electrospray ionization-mass spectrometry method, in which post-column pH adjustment and metal infusion are combined with ion identity molecular networking, a rule-based data analysis workflow. This method enabled the identification of metal-binding compounds in complex samples based on defined mass (m/z) offsets of ion species with the same chromatographic profiles. As this native electrospray metabolomics approach is suited to the use of any liquid chromatography-mass spectrometry system to explore the binding of any metal, this method has the potential to become an essential strategy for elucidating metal-binding molecules in biology.

Molecular networking connects mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. As a result, the fragmentation spectra of these ion species often remain unconnected in tandem mass spectrometry-based molecular networks, leading to redundant and disconnected sub-networks of the same compound classes. To overcome this bottleneck, we develop Ion Identity Molecular Networking (IIMN) that integrates chromatographic peak shape correlation analysis into molecular networks to connect and collapse different ion species of the same molecule. The new feature relationships improve network connectivity for structurally related molecules, can be used to reveal unknown ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral reference libraries. IIMN is integrated into various open source feature finding tools and the GNPS environment. Moreover, IIMN-based spectral libraries with a broad coverage of ion species are publicly available.

Urbanization along coastlines alters marine ecosystems including contributing molecules of anthropogenic origin to the coastal dissolved organic matter (DOM) pool. A broad assessment of the nature and extent of anthropogenic impacts on coastal ecosystems is urgently needed to inform regulatory guidelines and ecosystem management. Recently, non-targeted tandem mass spectrometry approaches are gaining momentum for the analysis of global organic matter composition (chemotypes) including a wide array of natural and anthropogenic compounds. In line with these efforts, we developed a non-targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) workflow that utilizes advanced data analysis approaches such as feature-based molecular networking and repository-scale spectrum searches. This workflow allows the scalable comparison and mapping of seawater chemotypes from large-scale spatial surveys as well as molecular family level annotation of unknown compounds. As a case study, we visualized organic matter chemotype shifts in coastal environments in northern San Diego, USA, after notable rain fall in winter 2017/2018 and highlight potential anthropogenic impacts. The observed seawater chemotype, consisting of 4384 LC-MS/MS features, shifted significantly after a major rain event. Molecular drivers of this shift could be attributed to multiple anthropogenic compounds, including pesticides (Imazapyr and Isoxaben), cleaning products (Benzyl-tetradecyl-dimethylammonium) and chemical additives (Hexa (methoxymethyl)melamine) and potential degradation products. By expanding the search of identified xenobiotics to other public tandem mass spectrometry datasets, we further contextualized their possible origin and show their importance in other ecosystems. The mass spectrometry and data analysis pipelines applied here offer a scalable framework for future molecular mapping and monitoring of marine ecosystems, which will contribute to a deliberate assessment of how chemical pollution impacts our oceans.

We investigated variability in the C:234Th ratio of sinking particles and its relationship to changing water column characteristics and plankton ecological dynamics during 29 Lagrangian experiments conducted on six cruises of the California Current Ecosystem Long-Term Ecological Research (CCE-LTER) Program. C:234Th ratios of sinking particles collected by a surface-tethered sediment trap (C:234ThST) varied from 2.3 to 20.5 μmol C dpm−1 over a depth range of 47–150 m. C:234ThST was significantly greater (by a factor of 1.8) than C:234Th ratios of suspended >51-μm particles collected in the same water parcels with in situ pumps. C:234Th ratios of large (>200-μm) sinking particles also exceeded those of smaller sinking particles. C:234ThST decreased with depth from the base of the euphotic zone through the upper twilight zone. C:234ThST was positively correlated with several indices of ecosystem productivity including particulate organic carbon (POC) and chlorophyll (Chl) concentrations, mesozooplankton biomass, and the fraction of Chl >20-μm. Principal component analysis and multiple linear regression suggested that decaying phytoplankton blooms exhibited higher C:234ThST than actively growing blooms at similar biomass levels. C:234ThST was positively correlated with indices of the fractional contribution of fecal pellets in sediment traps when the proportion of fecal pellets was low in the traps, likely because of a correlation between mesozooplankton biomass and other indices of ecosystem productivity. However, when fecal pellets were a more important component of sinking material, C:234ThST decreased with increasing fecal pellet content. C:234ThST was also positively correlated with the Si:C ratio of sinking particles. Across the dataset (and across depths) a strong correlation was found between C:234ThST and the ratio of vertically-integrated POC to vertically-integrated total water column 234Th (vC:234Thtot). A mechanistic one-layer, two-box model of thorium sorption and desorption was invoked to explain this correlation. Two empirical models (one using vC:234Thtot; one using depth and vertically-integrated Chl) were developed to predict C:234Th ratios in this coastal upwelling biome. The former regression (log10(C:234ThST) = 0.43 × log10(vC:234Thtot) + 0.53) was found to also be a reasonable predictor for C:234ThST from diverse regions including the Southern Ocean, Sargasso Sea, Subarctic North Pacific, and Eastern Tropical North Pacific.

The ocean's biota sequester atmospheric carbon dioxide (CO2) in part by producing dissolved organic matter (DOM) that persists in the ocean for millennia. This long-term accumulation of carbon may be facilitated by abiotic and biotic production of chemical structures that resist degradation, consequently contributing disproportionately to refractory DOM. Compounds that are selectively preserved in seawater were identified in solid-phase extracted DOM (PPL-DOM) using comprehensive gas chromatography (GC) coupled to mass spectrometry (MS). These molecules contained cyclic head groups that were linked to isoprenoid tails, and their overall structures closely resembled carotenoid degradation products (CDP). The origin of these compounds in PPL-DOM was further confirmed with an in vitro β-carotene photooxidation experiment that generated water-soluble CDP with similar structural characteristics. The molecular-level identification linked at least 10% of PPL-DOM carbon, and thus 4% of total DOM carbon, to CDP. Nuclear magnetic resonance spectra of experimental CDP and environmental PPL-DOM overlapped considerably, which indicated that even a greater proportion of PPL-DOM was likely composed of CDP. The CDP-rich DOM fraction was depleted in radiocarbon (14C age > 1500 years), a finding that supports the possible long-term accumulation of CDP in seawater. By linking a specific class of widespread biochemicals to refractory DOM, this work provides a foundation for future studies that aim to examine how persistent DOM forms in the ocean.

Enhanced vertical carbon transport (gravitational sinking and subduction) at mesoscale ocean fronts may explain the demonstrated imbalance of new production and sinking particle export in coastal upwelling ecosystems. Based on flux assessments from 238U:234Th disequilibrium and sediment traps, we found 2 to 3 times higher rates of gravitational particle export near a deep-water front (305 mg C⋅m-2⋅d-1) compared with adjacent water or to mean (nonfrontal) regional conditions. Elevated particle flux at the front was mechanistically linked to Fe-stressed diatoms and high mesozooplankton fecal pellet production. Using a data assimilative regional ocean model fit to measured conditions, we estimate that an additional ∼225 mg C⋅m-2⋅d-1 was exported as subduction of particle-rich water at the front, highlighting a transport mechanism that is not captured by sediment traps and is poorly quantified by most models and in situ measurements. Mesoscale fronts may be responsible for over a quarter of total organic carbon sequestration in the California Current and other coastal upwelling ecosystems.

There are few measurements of nitrification in polar regions, yet geochemical evidence suggests that it is significant, and chemoautotrophy supported by nitrification has been suggested as an important contribution to prokaryotic production during the polar winter. This study reports seasonal ammonia oxidation (AO) rates, gene and transcript abundance in continental shelf waters west of the Antarctic Peninsula, where Thaumarchaeota strongly dominate populations of ammonia-oxidizing organisms. Higher AO rates were observed in the late winter surface mixed layer compared with the same water mass sampled during summer (mean±s.e.: 62±16 versus 13±2.8 nm per day, t-test P

Targeted environmental monitoring reveals contamination by known chemicals, but may exclude potentially pervasive but unknown compounds. Marine mammals are sentinels of persistent and bioaccumulative contaminants due to their longevity and high trophic position. Using nontargeted analysis, we constructed a mass spectral library of 327 persistent and bioaccumulative compounds identified in blubber from two ecotypes of common bottlenose dolphins (Tursiops truncatus) sampled in the Southern California Bight. This library of halogenated organic compounds (HOCs) consisted of 180 anthropogenic contaminants, 41 natural products, 4 with mixed sources, 8 with unknown sources, and 94 with partial structural characterization and unknown sources. The abundance of compounds whose structures could not be fully elucidated highlights the prevalence of undiscovered HOCs accumulating in marine food webs. Eighty-six percent of the identified compounds are not currently monitored, including 133 known anthropogenic chemicals. Compounds related to dichlorodiphenyltrichloroethane (DDT) were the most abundant. Natural products were, in some cases, detected at abundances similar to anthropogenic compounds. The profile of naturally occurring HOCs differed between ecotypes, suggesting more abundant offshore sources of these compounds. This nontargeted analytical framework provided a comprehensive list of HOCs that may be characteristic of the region, and its application within monitoring surveys may suggest new chemicals for evaluation.

Water‐logged peatlands store tremendous amounts of soil carbon (C) globally, accumulating C over millennia. As peatlands become disturbed by human activity, these long‐term C stores are getting destabilized and ultimately released as greenhouse gases that may exacerbate climate change. Oxidation of the dissolved organic carbon (DOC) mobilized from disturbed soils to streams and canals may be one avenue for the transfer of previously stored, millennia‐aged C to the atmosphere. However, it remains unknown whether aged peat‐derived DOC undergoes oxidation to carbon dioxide (CO2) following disturbance. Here, we use a new approach to measure the radiocarbon content of CO2 produced from the oxidation of DOC in canals overlying peatland soils that have undergone widespread disturbance in Indonesia. This work shows for the first time that aged DOC mobilized from drained and burned peatland soils is susceptible to oxidation by both microbial respiration and photomineralization over aquatic travel times for DOC. The bulk radiocarbon age of CO2 produced during canal oxidation ranged from modern to ~1300 years before present. These ages for CO2 were most strongly influenced by canal water depth, which was proportional to the water table level where DOC is mobilized from disturbed soils to canals. Canal microbes preferentially respired older or younger organic C pools to CO2, and this may have been facilitated by the use of a small particulate organic C pool over the dissolved pool. Given that high densities of canals are generally associated with lower water tables and higher fire risk, our findings suggest that peatland areas with high canal density may be a hotspot for the loss of aged C on the landscape. Taken together, the results of this study show how and why aquatic processing of organic C on the landscape can enhance the transfer of long‐term peat C stores to the atmosphere following disturbance. [ABSTRACT FROM AUTHOR]

Hopanoids are pentacyclic triterpenoid lipids produced by many prokaryotes as cell membrane components. The structural variations of composite hopanoids, or bacteriohopanepolyols (BHPs), produced by various bacterial genera make them potentially useful molecular biomarkers of bacterial communities and metabolic processes in both modern and ancient environments. Building on previous work suggesting that organisms in low-oxygen environments are important contributors to BHP production in the marine water column and that there may be physiological roles for BHPs specific to these environments, this study investigated the relationship between trends in BHP structural diversity and abundance and the genetic diversity of BHP producers for the first time in a low-oxygen environment of the Eastern Tropical North Pacific. Amplification of the hopanoid biosynthesis gene for squalene hopene cyclase (sqhC) indicated far greater genetic diversity than would be predicted by examining BHP structural diversity alone and that greater sqhC genetic diversity exists in the marine environment than is represented by cultured representatives and most marine metagenomes. In addition, the genetic relationships in this data set suggest microaerophilic environments as potential "hot spots" of BHP production. Finally, structural analysis of BHPs showed that an isomer of the commonly observed BHP bacteriohopanetetrol may be linked to a producer that is more abundant in low-oxygen environments. Results of this study increase the known diversity of BHP producers and provide a detailed phylogeny with implications for the role of hopanoids in modern bacteria, as well as the evolutionary history of hopanoid biosynthesis, both of which are important considerations for future interpretations of the marine sedimentary record.

This paper describes the application of a novel, practical approach for isolation of individual compounds from complex organic matrices for natural abundance radiocarbon measurement. This is achieved through the use of automated preparative capillary gas chromatography (PCGC) to separate and recover sufficient quantities of individual target compounds for (14)C analysis by accelerator mass spectrometry (AMS). We developed and tested this approach using a suite of samples (plant lipids, petroleums) whose ages spanned the (14)C time scale and which contained a variety of compound types (fatty acids, sterols, hydrocarbons). Comparison of individual compound and bulk radiocarbon signatures for the isotopically homogeneous samples studied revealed that Δ(14)C values generally agreed well (±10%). Background contamination was assessed at each stage of the isolation procedure, and incomplete solvent removal prior to combustion was the only significant source of additional carbon. Isotope fractionation was addressed through compound-specific stable carbon isotopic analyses. Fractionation of isotopes during isolation of individual compounds was minimal (