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A large patch of anomalously warm water (nicknamed “the Blob”) appeared off the coast of Alaska in the winter of 2013–2014 and subsequently stretched south to Baja California. This northeastern Pacific warm-water anomaly persisted through the end of 2015. Scientists and the public alike noted widespread changes in the biological structure and composition of both openocean and coastal ecosystems. Changes included geographical shifts of species such as tropical copepods, pelagic red crabs, and tuna; closures of commercially important fisheries; and mass strandings of marine mammals and seabirds. The ecological responses to these physical changes have been sparsely quantified and are largely unknown. Here, we provide a bottom-up summary of some of the biological changes observed in and around the areas affected by the Blob.

Dissolved organic matter (DOM) is an ultracomplex mixture that plays a central role in global biogeochemical cycles. Despite its importance, DOM remains poorly understood at the molecular level. Over the last decades, significant efforts have been made to decipher the chemical composition of DOM by high-resolution mass spectrometry (HR-MS) and liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS). Yet, the complexity and high degree of nonresolved isomers still hamper the full structural analysis of DOM. To address this challenge, we developed an offline two-dimensional (2D) LC approach using two reversed-phase dimensions with orthogonal pH levels, followed by MS/MS data acquisition and molecular networking. 2D-LC-MS/MS reduced the complexity of DOM, enhancing the quality of MS/MS spectra and increasing spectral annotation rates. Applying our approach to analyze coastal-surface DOM from Southern California (USA) and open-ocean DOM from the central North Pacific (Hawaii), we annotated in total more than 600 structures via MS/MS spectrum matching, which was up to 90% more than that in iterative 1D LC-MS/MS analysis with the same total run time. Our data offer unprecedented insights into the molecular composition of marine DOM and highlight the potential of 2D-LC-MS/MS approaches to decipher the chemical composition of ultracomplex samples.

Coral bleaching is a well-documented and increasingly widespread phenomenon in reefs across the globe, yet there has been relatively little research on the implications for reef water column microbiology and biogeochemistry. A mesocosm heating experiment and bottle incubation compared how unbleached and bleached corals alter dissolved organic matter (DOM) exudation in response to thermal stress and subsequent effects on microbial growth and community structure in the water column. Thermal stress of healthy corals tripled DOM flux relative to ambient corals. DOM exudates from stressed corals (heated and/or previously bleached) were compositionally distinct from healthy corals and significantly increased growth of bacterioplankton, enriching copiotrophs and putative pathogens. Together these results demonstrate how the impacts of both short-term thermal stress and long-term bleaching may extend into the water column, with altered coral DOM exudation driving microbial feedbacks that influence how coral reefs respond to and recover from mass bleaching events., (© 2024. The Author(s).)

Recent developments in molecular networking have expanded our ability to characterize the metabolome of diverse samples that contain a significant proportion of ion features with no mass spectral match to known compounds. Manual and tool-assisted natural annotation propagation is readily used to classify molecular networks; however, currently no annotation propagation tools leverage consensus confidence strategies enabled by hierarchical chemical ontologies or enable the use of new in silico tools without significant modification. Herein we present ConCISE (Consensus Classifications of In Silico Elucidations) which is the first tool to fuse molecular networking, spectral library matching and in silico class predictions to establish accurate putative classifications for entire subnetworks. By limiting annotation propagation to only structural classes which are identical for the majority of ion features within a subnetwork, ConCISE maintains a true positive rate greater than 95% across all levels of the ChemOnt hierarchical ontology used by the ClassyFire annotation software (superclass, class, subclass). The ConCISE framework expanded the proportion of reliable and consistent ion feature annotation up to 76%, allowing for improved assessment of the chemo-diversity of dissolved organic matter pools from three complex marine metabolomics datasets comprising dominant reef primary producers, five species of the diatom genus Pseudo-nitzchia, and stromatolite sediment samples.

The exchange of metabolites mediates algal and bacterial interactions that maintain ecosystem function. Yet, while thousands of metabolites are produced, only a few molecules have been identified in these associations. Using the ubiquitous microalgae Pseudo-nitzschia sp., as a model, we employed an untargeted metabolomics strategy to assign structural characteristics to the metabolites that distinguished specific diatom-microbiome associations. We cultured five species of Pseudo-nitzschia, including two species that produced the toxin domoic acid, and examined their 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 and amides 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 facilitate microbial partnerships and uncovers the chemical diversity that underpins algae-bacteria interactions., (© 2022 Applied Microbiology International and John Wiley & Sons Ltd.)

Metabolites exuded by primary producers comprise a significant fraction of marine dissolved organic matter, a poorly characterized, heterogenous mixture that dictates microbial metabolism and biogeochemical cycling. We present a foundational untargeted molecular analysis of exudates released by coral reef primary producers using liquid chromatography-tandem mass spectrometry to examine compounds produced by two coral species and three types of algae (macroalgae, turfing microalgae, and crustose coralline algae [CCA]) from Mo'orea, French Polynesia. Of 10,568 distinct ion features recovered from reef and mesocosm waters, 1,667 were exuded by producers; the majority (86%) were organism specific, reflecting a clear divide between coral and algal exometabolomes. These data allowed us to examine two tenets of coral reef ecology at the molecular level. First, stoichiometric analyses show a significantly reduced nominal carbon oxidation state of algal exometabolites than coral exometabolites, illustrating one ecological mechanism by which algal phase shifts engender fundamental changes in the biogeochemistry of reef biomes. Second, coral and algal exometabolomes were differentially enriched in organic macronutrients, revealing a mechanism for reef nutrient-recycling. Coral exometabolomes were enriched in diverse sources of nitrogen and phosphorus, including tyrosine derivatives, oleoyl-taurines, and acyl carnitines. Exometabolites of CCA and turf algae were significantly enriched in nitrogen with distinct signals from polyketide macrolactams and alkaloids, respectively. Macroalgal exometabolomes were dominated by nonnitrogenous compounds, including diverse prenol lipids and steroids. This study provides molecular-level insights into biogeochemical cycling on coral reefs and illustrates how changing benthic cover on reefs influences reef water chemistry with implications for microbial metabolism., Competing Interests: The authors declare no competing interest., (Copyright © 2022 the Author(s). Published by PNAS.)

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.

Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. FBMN enables quantitative analysis and resolution of isomers, including from ion mobility spectrometry.

Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule-focused tandem mass spectrometry (MS 2 ) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS 2 dataset and to connect this chemical insight to the user's underlying biological questions. This can be performed within one liquid chromatography (LC)-MS 2 experiment or at the repository scale. GNPS-MassIVE is a public data repository for untargeted MS 2 data with sample information (metadata) and annotated MS 2 spectra. These publicly accessible data can be annotated and updated with the GNPS infrastructure keeping a continuous record of all changes. This knowledge is disseminated across all public data; it is a living dataset. Molecular networking-one of the main analysis tools used within the GNPS platform-creates a structured data table that reflects the molecular diversity captured in tandem mass spectrometry experiments by computing the relationships of the MS 2 spectra as spectral similarity. This protocol provides step-by-step instructions for creating reproducible, high-quality molecular networks. For training purposes, the reader is led through a 90- to 120-min procedure that starts by recalling an example public dataset and its sample information and proceeds to creating and interpreting a molecular network. Each data analysis job can be shared or cloned to disseminate the knowledge gained, thus propagating information that can lead to the discovery of molecules, metabolic pathways, and ecosystem/community interactions.

In our daily lives, we consume foods that have been transported, stored, prepared, cooked, or otherwise processed by ourselves or others. Food storage and preparation have drastic effects on the chemical composition of foods. Untargeted mass spectrometry analysis of food samples has the potential to increase our chemical understanding of these processes by detecting a broad spectrum of chemicals. We performed a time-based analysis of the chemical changes in foods during common preparations, such as fermentation, brewing, and ripening, using untargeted mass spectrometry and molecular networking. The data analysis workflow presented implements an approach to study changes in food chemistry that can reveal global alterations in chemical profiles, identify changes in abundance, as well as identify specific chemicals and their transformation products. The data generated in this study are publicly available, enabling the replication and re-analysis of these data in isolation, and serve as a baseline dataset for future investigations., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

The cars we drive, the homes we live in, the restaurants we visit, and the laboratories and offices we work in are all a part of the modern human habitat. Remarkably, little is known about the diversity of chemicals present in these environments and to what degree molecules from our bodies influence the built environment that surrounds us and vice versa. We therefore set out to visualize the chemical diversity of five built human habitats together with their occupants, to provide a snapshot of the various molecules to which humans are exposed on a daily basis. The molecular inventory was obtained through untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of samples from each human habitat and from the people that occupy those habitats. Mapping MS-derived data onto 3D models of the environments showed that frequently touched surfaces, such as handles (e.g., door, bicycle), resemble the molecular fingerprint of the human skin more closely than other surfaces that are less frequently in direct contact with humans (e.g., wall, bicycle frame). Approximately 50% of the MS/MS spectra detected were shared between people and the environment. Personal care products, plasticizers, cleaning supplies, food, food additives, and even medications that were found to be a part of the human habitat. The annotations indicate that significant transfer of chemicals takes place between us and our built environment. The workflows applied here will lay the foundation for future studies of molecular distributions in medical, forensic, architectural, space exploration, and environmental applications.

Remineralization and transformation of dissolved organic matter (DOM) by marine microbes shape the DOM composition and thus, have large impact on global carbon and nutrient cycling. However, information on bacterioplankton-DOM interactions on a molecular level is limited. We examined the variation of bacterial community composition (BCC) at Helgoland Roads (North Sea) in relation to variation of molecular DOM composition and various environmental parameters on short-time scales. Surface water samples were taken daily over a period of 20 days. Bacterial community and molecular DOM composition were assessed via 16S rRNA gene tag sequencing and ultrahigh resolution Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), respectively. Environmental conditions were driven by a coastal water influx during the first half of the sampling period and the onset of a summer phytoplankton bloom toward the end of the sampling period. These phenomena led to a distinct grouping of bacterial communities and DOM composition which was particularly influenced by total dissolved nitrogen (TDN) concentration, temperature, and salinity, as revealed by distance-based linear regression analyses. Bacterioplankton-DOM interaction was demonstrated in strong correlations between specific bacterial taxa and particular DOM molecules, thus, suggesting potential specialization on particular substrates. We propose that a combination of high resolution techniques, as used in this study, may provide substantial information on substrate generalists and specialists and thus, contribute to prediction of BCC variation.

Background: Pulmonary vein isolation (PVI) is an established treatment option for atrial fibrillation (AF). Recently the novel endoscopic ablation system (EAS) was introduced and proved potential for successful acute PVI., Objective: This study sought to investigate the 1-year follow-up results after EAS-based PVI., Methods: A total of 40 patients (20 female, age 57 ± 9 years) with a long history (5 ± 4 years) of drug-refractory (2 ± 1 antiarrhythmic drugs) paroxysmal AF were included into our analysis. PVI was performed using exclusively the novel EAS. Follow-up included regular telephonic interviews, Holter electrocardiographic (ECG) and transtelephonic ECG recordings. A symptomatic or documented AF episode >60 seconds after a blanking period of 3 months was defined as recurrence., Results: A total of 155 PVs were targeted; 153 of 155 (99%) PVs were isolated successfully using exclusively the novel EAS. During a median follow-up of 402 (331 to 478; quartile 1 to quartile 3) days, 24 of 40 patients (60%) remained free of any symptomatic or documented AF episode without antiarrhythmic drugs after a single procedure. Seven patients suffering from AF recurrence underwent radiofrequency current-based Re-PVI 203 ± 102 days after the index EAS-based procedure. Left atrium to pulmonary vein reconduction was found in 17 of 25 initially isolated PVs. No PV stenosis was detected based on magnetic resonance imaging 3 months postablation., Conclusion: Patients after EAS-based PVI due to paroxysmal AF demonstrate 1-year single-procedure success rates similar to those of other ablation techniques and ablation energies. The major determinant for AF recurrence after EAS treatment seems to be reconnection of previously isolated PVs. More patients and longer follow-up periods are mandatory before final conclusions can be drawn regarding the efficacy and safety of the EAS., (Copyright © 2011 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.)

Background: Pulmonary vein isolation (PVI) is an established treatment option for paroxysmal atrial fibrillation. Recently, a novel endoscopic ablation system (EAS) was introduced. The incidence and severity of ablation-induced esophageal thermal lesions (ETLs) are unknown., Objective: The purpose of this study was to investigate the incidence and severity of ablation-induced ETLs., Methods: This prospective analysis compared two groups: group A underwent EAS-based PVI, and group B received PVI using radio frequency current (RFC). If esophageal temperature measured via an endoluminal temperature probe exceeded 38.5°C, energy application was stopped immediately. Endoscopy was performed 2 days postablation., Results: Forty patients (20 female, mean age 56 ± 10 years) were treated with the EAS system (group A). In 20 patients (seven female, mean age 63 ± 9 years) RFC-based PVI was performed (group B). Esophageal endoscopy was performed 2.1 ± 0.8 (group A) and 2.8 ± 1.2 days postablation (group B), respectively. In 7/40 patients (18%) in group A, thermal lesions (four thermal ulcerations, three minimal thermal lesions) were detected. In group B, 3/20 patients (15%) displayed thermal lesions (three minimal thermal lesions). All thermal lesions resolved upon repeat endoscopy performed 8 ± 6 (group A) and 5 ± 1 days (group B) after initial endoscopy., Conclusion: In the EAS group, ETLs were found in 18% of patients, as compared with in 15% in the RFC group. In patients with ETLs, ulcerations were found in 57% in the EAS group, as compared with 0% in the RFC group. This may indicate that the quality of thermal lesions is more severe in the EAS group. Further investigation is required., (Copyright © 2011 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.)

Introduction: Circumferential pulmonary vein isolation (CPVI) is associated with a high success rate in patients with paroxysmal and persistent atrial fibrillation (AF). However, in patients with long-standing persistent AF, the ideal ablation strategy still remains a matter of debate., Methods and Results: Two-hundred and five patients underwent catheter ablation for long-standing persistent AF defined as continuous AF of more than 1-year duration. In a first step, all patients underwent CPVI. If direct-current cardioversion failed following CPVI, ablation of complex fractionated atrial electrograms (CFAEs) was performed. The goal was conversion into sinus rhythm (SR) or, alternatively, atrial tachycardia (AT) with subsequent ablation. A total of 340 procedures were performed. CPVI alone was performed during 165 procedures in 124 of 205 (60.5%) patients. In the remaining 81 patients, additional CFAE ablation was performed in 45, left linear lesions for recurrent ATs in 44 and SVC isolation in 15 patients, respectively, resulting in inadvertent left atrial appendage isolation in 9 (4.4%) patients. After the initial ablation procedure, 67 of 199 patients remained in SR during a mean follow-up of 19 ± 11 months. Six patients were lost to follow-up. After a mean of 1.7 ± 0.8 procedures, 135 of 199 patients (67.8%) remained in SR. Eighty-six patients (43.2%) remained in SR following CPVI performed as the sole ablative strategy., Conclusions: CPVI alone is sufficient to restore SR in 43.2% of patients with long-standing persistent AF. Multiple procedures and additional ablation strategies with a significant risk of inadvertent left atrial appendage isolation are often required to maintain stable SR., (© 2010 Wiley Periodicals, Inc.)

Aims: High-intensity focused ultrasound (HIFU) applied via a balloon catheter is a novel technology for pulmonary vein isolation (PVI) in patients with paroxysmal atrial fibrillation (PAF). The long-term success rate is unknown., Methods and Results: Thirty-two patients (22 male, age 60 +/- 9 years) with a long history [5 (4;9) years] of drug refractory [3 +/- 1 anti-arrhythmic drugs (AADs)], symptomatic PAF were included into the analysis. Pulmonary vein isolation was performed using the first- and second-generation HIFU balloon catheters (ProRhythm, Ronkonkoma, NY, USA). Follow-up (F/U) included regular telephonic interviews, trans-telephonic Holter ECG, and event recording. Recurrence was defined as a documented or symptomatic AF episode >30 s without a blanking period. In total 101/116 targeted PVs (87%) were acutely isolated exclusively using HIFU. During a median F/U of 1400 (930;1568) days, 18 patients (56%) were free of AF without AAD after a single HIFU procedure. In nine patients with AF recurrence, 20 PVs exhibited electrical reconduction and re-isolation was performed using irrigated radiofrequency current (RFC) ablation., Conclusion: Patients treated with the first- and second-generation HIFU balloon catheters due to symptomatic PAF show long-term success rates similar to RFC-based PVI procedures. The major determinant of AF recurrence after HIFU treatment seems to be reconduction of previously isolated PVs. However, the favourable effectiveness is offset by the severe complications reported following HIFU treatment. This led to a halt of its clinical use.