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Article ; Online: Coral thermal stress and bleaching enrich and restructure reef microbial communities via altered organic matter exudation.

Sparagon, Wesley J / Arts, Milou G I / Quinlan, Zachary A / Wegley Kelly, Linda / Koester, Irina / Comstock, Jacqueline / Bullington, Jessica A / Carlson, Craig A / Dorrestein, Pieter C / Aluwihare, Lihini I / Haas, Andreas F / Nelson, Craig E

Communications biology

2024 Volume 7, Issue 1, Page(s) 160

Abstract: 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 ...

Abstract	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.
MeSH term(s)	Animals ; Anthozoa/physiology ; Coral Reefs ; Hot Temperature ; Water
Chemical Substances	Water (059QF0KO0R)
Language	English
Publishing date	2024-02-13
Publishing country	England
Document type	Journal Article
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-023-05730-0
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Article: ConCISE: Consensus Annotation Propagation of Ion Features in Untargeted Tandem Mass Spectrometry Combining Molecular Networking and

Quinlan, Zachary A / Koester, Irina / Aron, Allegra T / Petras, Daniel / Aluwihare, Lihini I / Dorrestein, Pieter C / Nelson, Craig E / Wegley Kelly, Linda

Metabolites

2022 Volume 12, Issue 12

Abstract: 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 ...

Abstract	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
Language	English
Publishing date	2022-12-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662251-8
ISSN	2218-1989
ISSN	2218-1989
DOI	10.3390/metabo12121275
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Article ; Online: Illuminating the dark metabolome of Pseudo‐nitzschia–microbiome associations

Koester, Irina / Quinlan, Zachary A. / Nothias, Louis‐Félix / White, Margot E. / Rabines, Ariel / Petras, Daniel / Brunson, John K. / Dührkop, Kai / Ludwig, Marcus / Böcker, Sebastian / Azam, Farooq / Allen, Andrew E. / Dorrestein, Pieter C. / Aluwihare, Lihini I.

Environmental Microbiology. 2022 Nov., v. 24, no. 11 p.5408-5424

2022

Abstract: 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 ... ...

Abstract	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.
Keywords	Pseudo-nitzschia ; computer simulation ; domoic acid ; ecological function ; imidazoles ; lactams ; metabolites ; metabolome ; metabolomics ; microalgae ; microbiology ; microbiome ; models ; nitrogen ; pyrrolidines ; tandem mass spectrometry ; toxins
Language	English
Dates of publication	2022-11
Size	p. 5408-5424.
Publishing place	John Wiley & Sons, Inc.
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.16242
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Article ; Online: Illuminating the dark metabolome of Pseudo-nitzschia-microbiome associations.

Koester, Irina / Quinlan, Zachary A / Nothias, Louis-Félix / White, Margot E / Rabines, Ariel / Petras, Daniel / Brunson, John K / Dührkop, Kai / Ludwig, Marcus / Böcker, Sebastian / Azam, Farooq / Allen, Andrew E / Dorrestein, Pieter C / Aluwihare, Lihini I

Environmental microbiology

2022 Volume 24, Issue 11, Page(s) 5408–5424

Abstract	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.
MeSH term(s)	Diatoms/metabolism ; Microbiota ; Tandem Mass Spectrometry ; Metabolome
Language	English
Publishing date	2022-11-01
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.16242
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Article ; Online: Distinguishing the molecular diversity, nutrient content, and energetic potential of exometabolomes produced by macroalgae and reef-building corals.

Wegley Kelly, Linda / Nelson, Craig E / Petras, Daniel / Koester, Irina / Quinlan, Zachary A / Arts, Milou G I / Nothias, Louis-Felix / Comstock, Jacqueline / White, Brandie M / Hopmans, Ellen C / van Duyl, Fleur C / Carlson, Craig A / Aluwihare, Lihini I / Dorrestein, Pieter C / Haas, Andreas F

Proceedings of the National Academy of Sciences of the United States of America

2022 Volume 119, Issue 5

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Animals ; Anthozoa/genetics ; Anthozoa/growth & development ; Anthozoa/metabolism ; Carbon/metabolism ; Coral Reefs ; Dissolved Organic Matter/analysis ; Ecosystem ; Marine Biology/methods ; Metabolomics/methods ; Nitrogen/metabolism ; Nutrients ; Phosphorus/metabolism ; Polynesia ; Seawater/chemistry ; Seaweed/genetics ; Seaweed/growth & development ; Seaweed/metabolism
Chemical Substances	Dissolved Organic Matter ; Phosphorus (27YLU75U4W) ; Carbon (7440-44-0) ; Nitrogen (N762921K75)
Language	English
Publishing date	2022-01-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2110283119
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Article: Short-Term Dynamics of North Sea Bacterioplankton-Dissolved Organic Matter Coherence on Molecular Level.

Lucas, Judith / Koester, Irina / Wichels, Antje / Niggemann, Jutta / Dittmar, Thorsten / Callies, Ulrich / Wiltshire, Karen H / Gerdts, Gunnar

Frontiers in microbiology

2016 Volume 7, Page(s) 321

Abstract: 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 ...

Abstract	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.
Language	English
Publishing date	2016-03-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2016.00321
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Article ; Online: Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment.

Schmid, Robin / Petras, Daniel / Nothias, Louis-Félix / Wang, Mingxun / Aron, Allegra T / Jagels, Annika / Tsugawa, Hiroshi / Rainer, Johannes / Garcia-Aloy, Mar / Dührkop, Kai / Korf, Ansgar / Pluskal, Tomáš / Kameník, Zdeněk / Jarmusch, Alan K / Caraballo-Rodríguez, Andrés Mauricio / Weldon, Kelly C / Nothias-Esposito, Melissa / Aksenov, Alexander A / Bauermeister, Anelize /

Albarracin Orio, Andrea / Grundmann, Carlismari O / Vargas, Fernando / Koester, Irina / Gauglitz, Julia M / Gentry, Emily C / Hövelmann, Yannick / Kalinina, Svetlana A / Pendergraft, Matthew A / Panitchpakdi, Morgan / Tehan, Richard / Le Gouellec, Audrey / Aleti, Gajender / Mannochio Russo, Helena / Arndt, Birgit / Hübner, Florian / Hayen, Heiko / Zhi, Hui / Raffatellu, Manuela / Prather, Kimberly A / Aluwihare, Lihini I / Böcker, Sebastian / McPhail, Kerry L / Humpf, Hans-Ulrich / Karst, Uwe / Dorrestein, Pieter C

Nature communications

2021 Volume 12, Issue 1, Page(s) 3832

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Animals ; Computational Biology/methods ; Internet ; Ions/chemistry ; Ions/metabolism ; Mass Spectrometry/methods ; Metabolic Networks and Pathways ; Metabolomics/methods ; Molecular Structure ; Reproducibility of Results ; Software
Chemical Substances	Ions
Language	English
Publishing date	2021-06-22
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-23953-9
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Article ; Online: Reproducible molecular networking of untargeted mass spectrometry data using GNPS.

Aron, Allegra T / Gentry, Emily C / McPhail, Kerry L / Nothias, Louis-Félix / Nothias-Esposito, Mélissa / Bouslimani, Amina / Petras, Daniel / Gauglitz, Julia M / Sikora, Nicole / Vargas, Fernando / van der Hooft, Justin J J / Ernst, Madeleine / Kang, Kyo Bin / Aceves, Christine M / Caraballo-Rodríguez, Andrés Mauricio / Koester, Irina / Weldon, Kelly C / Bertrand, Samuel / Roullier, Catherine /

Nature protocols

2020 Volume 15, Issue 6, Page(s) 1954–1991

Abstract: Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule-focused tandem mass spectrometry ( ... ...

Abstract	Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule-focused tandem mass spectrometry (MS
MeSH term(s)	Animals ; Chromatography, Liquid/methods ; Humans ; Metabolic Networks and Pathways ; Metabolomics/methods ; Mice ; Reproducibility of Results ; Software ; Tandem Mass Spectrometry/methods ; Workflow
Language	English
Publishing date	2020-05-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2244966-8
ISSN	1750-2799 ; 1754-2189
ISSN (online)	1750-2799
ISSN	1754-2189
DOI	10.1038/s41596-020-0317-5
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Article: Untargeted Mass Spectrometry-Based Metabolomics Approach Unveils Molecular Changes in Raw and Processed Foods and Beverages

Gauglitz, Julia M / Aceves, Christine M / Aksenov, Alexander A / Aleti, Gajender / Almaliti, Jehad / Bandeira, Nuno / Bouslimani, Amina / Brown, Elizabeth A / Campeau, Anaamika / Chaar, Rama / da Silva, Ricardo R / Demko, Alyssa M / Di Ottavio, Francesca / Dorrestein, Pieter C / Elijah, Emmanuel / Ernst, Madeleine / Holmes, Xavier / Jarmusch, Alan K / Jiang, Lingjing /

Kang, Kyo Bin / Koester, Irina / Kwan, Brian / Li, Jie / Li, Yueying / Mauricio Caraballo-Rodríguez, Andrés / Melnik, Alexey V / Molina-Santiago, Carlos / Ni, Bohan / Oom, Aaron L / Paige Ferguson, L / Panitchpakdi, Morgan W / Petras, Daniel / Quinn, Robert / Sikora, Nicole / Spengler, Katharina / Teke, Bahar / Tripathi, Anupriya / Ul-Hasan, Sabah / van der Hooft, Justin J.J / Vargas, Fernando / Vrbanac, Alison / Vu, Anthony Q / Wang, Steven C / Weldon, Kelly / Wilson, Kayla / Wozniak, Jacob M / Yoon, Michael

Food chemistry. 2019 July 28,

2019

Abstract: 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 ...

Abstract	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.
Keywords	beverages ; brewing ; chemical composition ; data collection ; fermentation ; food chemistry ; food composition ; food storage ; mass spectrometry ; metabolomics ; processed foods ; ripening
Language	English
Dates of publication	2019-0728
Publishing place	Elsevier Ltd
Document type	Article
Note	Pre-press version
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2019.125290
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Article ; Online: Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages.

Gauglitz, Julia M / Aceves, Christine M / Aksenov, Alexander A / Aleti, Gajender / Almaliti, Jehad / Bouslimani, Amina / Brown, Elizabeth A / Campeau, Anaamika / Caraballo-Rodríguez, Andrés Mauricio / Chaar, Rama / da Silva, Ricardo R / Demko, Alyssa M / Di Ottavio, Francesca / Elijah, Emmanuel / Ernst, Madeleine / Ferguson, L Paige / Holmes, Xavier / Jarmusch, Alan K / Jiang, Lingjing /

Kang, Kyo Bin / Koester, Irina / Kwan, Brian / Li, Jie / Li, Yueying / Melnik, Alexey V / Molina-Santiago, Carlos / Ni, Bohan / Oom, Aaron L / Panitchpakdi, Morgan W / Petras, Daniel / Quinn, Robert / Sikora, Nicole / Spengler, Katharina / Teke, Bahar / Tripathi, Anupriya / Ul-Hasan, Sabah / van der Hooft, Justin J J / Vargas, Fernando / Vrbanac, Alison / Vu, Anthony Q / Wang, Steven C / Weldon, Kelly / Wilson, Kayla / Wozniak, Jacob M / Yoon, Michael / Bandeira, Nuno / Dorrestein, Pieter C

Food chemistry

2019 Volume 302, Page(s) 125290

Abstract	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.
MeSH term(s)	Beverages/analysis ; Fermentation ; Food Analysis ; Food Handling ; Mass Spectrometry ; Metabolomics ; Workflow
Language	English
Publishing date	2019-07-30
Publishing country	England
Document type	Journal Article
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2019.125290
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