@article {azizah_2-homoectoine_2023,
	title = {2-Homoectoine: An Additional Member of the Ectoine Family from Phyto- and Bacterioplankton Involved in Osmoadaptation},
	journal = {Journal of Natural Products},
	year = {2023},
	note = {Publisher: American Chemical Society},
	month = {dec},
	abstract = {Ectoine is a central osmolyte in marine plankton due to its excellent cytoprotective traits and its multifunctional roles supporting the survival of microalgae and bacteria under unfavorable environmental conditions. The protective effect of ectoine toward several kinds of stresses stirred interest in biotechnology, pharmacy, and other fields including cosmetics. Also, its hydroxylated derivative, 5-hydroxyectoine, exhibits functions similar to ectoine. Here we introduce a molecular networking-based approach to expand the family of ectoine derivatives from phyto- and bacterioplankton. A ZIC-HILIC separation protocol coupled with HRMS/MS-based molecular networking allowed us to identify the new ectoine derivative 1,4,5,6-tetrahydro-2-ethyl-4-pyrimidinecarboxylic acid, or 2-homoectoine (1). 1 is found in many algae including dinoflagellates, chlorophytes, and haptophytes. In axenic strains, the content of 1 is substantially lower. In accordance, we found that marine bacteria are prolific producers of the compound as well. This suggests that the microalgae with their associated microbiome have to be considered as sources of the compound. Increasing concentrations of the compound under high salinity suggest a role as a protectant against osmotic stress.},
	keywords = {RCC131, RCC3579},
	issn = {0163-3864},
	doi = {10.1021/acs.jnatprod.3c00766},
	url = {https://doi.org/10.1021/acs.jnatprod.3c00766},
	author = {Azizah, Muhaiminatul and Pohnert, Georg}
}
@article {syhapanha_transcriptomicsguided_2023,
	title = {Transcriptomics-guided identification of an algicidal protease of the marine bacterium Kordia algicida OT-1},
	journal = {MicrobiologyOpen},
	volume = {12},
	number = {5},
	year = {2023},
	pages = {e1387},
	abstract = {In recent years, interest in algicidal bacteria has risen due to their ecological importance and their potential as biotic regulators of harmful algal blooms. Algicidal bacteria shape the plankton communities of the oceans by inhibiting or lysing microalgae and by consuming the released nutrients. Kordia algicida strain OT-1 is a model marine algicidal bacterium that was isolated from a bloom of the diatom Skeletonema costatum. Previous work has suggested that algicidal activity is mediated by secreted proteases. Here, we utilize a transcriptomics-guided approach to identify the serine protease gene KAOT1_RS09515, hereby named alpA1 as a key element in the algicidal activity of K. algicida. The protease AlpA1 was expressed and purified from a heterologous host and used in in vitro bioassays to validate its activity. We also show that K. algicida is the only algicidal species within a group of four members of the Kordia genus. The identification of this algicidal protease opens the possibility of real-time monitoring of the ecological impact of algicidal bacteria in natural phytoplankton blooms., Algicidal bacteria shape the plankton communities of the oceans by lysing microalgae and consuming the released nutrients. Kordia algicida is an environmentally relevant marine bacterium whose algicidal activity is mediated by secreted proteases. In this study, we utilize a transcriptomics-guided approach to identify the secreted serine protease AlpA1 as a key factor in the algicidal process. This discovery offers new approaches for the real-time monitoring and manipulation of algicidal bacteria in algal blooms.},
	keywords = {RCC75},
	issn = {2045-8827},
	doi = {10.1002/mbo3.1387},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10565126/},
	author = {Syhapanha, Kristy S. and Russo, David A. and Deng, Yun and Meyer, Nils and Poulin, Remington X. and Pohnert, Georg}
}
@article {sorokina_draft_2022,
	title = {Draft genome assembly and sequencing dataset of the marine diatom Skeletonema costatum RCC75},
	journal = {Data in Brief},
	year = {2022},
	month = {feb},
	pages = {107931},
	abstract = {Diatoms (Bacillariophyceae) are a major constituent of the phytoplankton and have a universally recognized ecological importance. Between 1,000 and 1,300 diatom genera have been described in the literature, but only 10 nuclear genomes have been published and made available to the public up to date. Skeletonema costatum is a cosmopolitan marine diatom, principally occurring in coastal regions, and is one of the most abundant members of the Skeletonema genus. Here we present a draft assembly of the Skeletonema costatum RCC75 genome, obtained from PacBio and Illumina NovaSeq data. This dataset will expand the knowledge of the Bacillariophyceae genetics and contribute to the global understanding of phytoplankton{\textquoteright}s physiological, ecological, and environmental functioning.},
	keywords = {Algal genome, BACILLARIOPHYCEAE, diatoms, genome sequencing, Illumina sequencing, PacBio sequencing, RCC75},
	issn = {2352-3409},
	doi = {10.1016/j.dib.2022.107931},
	url = {https://www.sciencedirect.com/science/article/pii/S2352340922001433},
	author = {Sorokina, Maria and Barth, Emanuel and Zulfiqar, Mahnoor and Kwantes, Michiel and Pohnert, Georg and Steinbeck, Christoph}
}
@article {nikitashina_metabolic_2022,
	title = {Metabolic adaptation of diatoms to hypersalinity},
	journal = {Phytochemistry},
	year = {2022},
	pages = {113267},
	abstract = {Microalgae are important primary producers and form the basis for the marine food web. As global climate changes, so do salinity levels that algae are exposed to. A metabolic response of algal cells partly alleviates the resulting osmotic stress. Some metabolites involved in the response are well studied, but the full metabolic implications of adaptation remain unclear. Improved analytical methodology provides an opportunity for additional insight. We can now follow responses to stress in major parts of the metabolome and derive comprehensive charts of the resulting metabolic re-wiring. In this study, we subjected three species of diatoms to high salinity conditions and compared their metabolome to controls in an untargeted manner. The three well-investigated species with sequenced genomes Phaeodactylum tricornutum, Thalassiosira pseudonana, and Skeletonema marinoi were selected for our survey. The microalgae react to salinity stress with common adaptations in the metabolome by amino acid up-regulation, production of saccharides, and inositols. But also species-specific dysregulation of metabolites is common. Several metabolites previously not connected with osmotic stress reactions are identified, including 4-hydroxyproline, pipecolinic acid, myo-inositol, threonic acid, and acylcarnitines. This expands our knowledge about osmoadaptation and calls for further functional characterization of metabolites and pathways in algal stress physiology.},
	keywords = {Diatomic algae, Hypersalinity stress response, Osmolytes, Phaeodactylaceae, Phaeodactylum tricornutum, RCC75, Skeletonema marinoi, Skeletonemataceae, Thalassiosira pseudonana, Thalassiosiraceae, Untargeted metabolite profiling},
	issn = {0031-9422},
	doi = {10.1016/j.phytochem.2022.113267},
	url = {https://www.sciencedirect.com/science/article/pii/S0031942222001832},
	author = {Nikitashina, Vera and Stettin, Daniel and Pohnert, Georg}
}
@article {azizah_orchestrated_2022,
	title = {Orchestrated Response of Intracellular Zwitterionic Metabolites in Stress Adaptation of the Halophilic Heterotrophic Bacterium Pelagibaca bermudensis},
	journal = {Marine Drugs},
	volume = {20},
	number = {11},
	year = {2022},
	month = {nov},
	pages = {727},
	abstract = {Osmolytes are naturally occurring organic compounds that protect cells against various forms of stress. Highly polar, zwitterionic osmolytes are often used by marine algae and bacteria to counteract salinity or temperature stress. We investigated the effect of several stress conditions including different salinities, temperatures, and exposure to organic metabolites released by the alga Tetraselmis striata on the halophilic heterotrophic bacterium Pelagibaca bermudensis. Using ultrahigh-performance liquid chromatography (UHPLC) on a ZIC-HILIC column and high-resolution electrospray ionization mass spectrometry, we simultaneously detected and quantified the eleven highly polar compounds dimethylsulfoxonium propionate (DMSOP), dimethylsulfoniopropionate (DMSP), gonyol, cysteinolic acid, ectoine, glycine betaine (GBT), carnitine, sarcosine, choline, proline, and 4-hydroxyproline. All compounds are newly described in P. bermudensis and potentially involved in physiological functions essential for bacterial survival under variable environmental conditions. We report that adaptation to various forms of stress is accomplished by adjusting the pattern and amount of the zwitterionic metabolites.},
	keywords = {RCC131},
	issn = {1660-3397},
	doi = {10.3390/md20110727},
	url = {https://www.mdpi.com/1660-3397/20/11/727},
	author = {Azizah, Muhaiminatul and Pohnert, Georg}
}
@article {meyer_pronounced_2022,
	title = {Pronounced Uptake and Metabolism of Organic Substrates by Diatoms Revealed by Pulse-Labeling Metabolomics},
	journal = {Frontiers in Marine Science},
	volume = {9},
	year = {2022},
	pages = {821167},
	abstract = {Diatoms contribute as a dominant group of microalgae to approximately 20\% of the global carbon fixation. In the plankton, these photosynthetic algae are exposed to a plethora of metabolites, especially when competing algae are lysed. It is well established that diatoms can take up specific metabolites, such as vitamins, amino acids as nitrogen source, or dimethylsulfoniopropoionate to compensate for changes in water salinity. It is, however, unclear to which extent diatoms take up other organic resources and if these are incorporated into the cell{\textasciiacute}s metabolism. Here, we explore the general scope of uptake of metabolites from competitors. Using labeled metabolites released during lysis of algae grown under a 13CO2 atmosphere, we show that the cosmopolitan diatom Chaetoceros didymus takes up even dilute organic substrates from these lysates with little bias for molecular weight or polarity. This is reflected by a high degree of labeling in the metabolome of the exposed cells. The newly developed pulse label/mass spectrometry metabolomics approach reveals that polarity and molecular weight has no detectable influence on uptake. We further show that the taken-up metabolites are partly maintained without metabolic modification within the cells, but also a substantial part is subject to catabolic and anabolic transformation. One of the most dominant phytoplankton groups thus has the potential to compete with heterotrophs, suggesting that the observed osmotrophy may substantially impact organic material fluxes in the oceans. Our findings call for the refinement of our understanding of competition in the plankton.},
	keywords = {RCC75},
	issn = {2296-7745},
	doi = {10.3389/fmars.2022.821167},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2022.821167/full},
	author = {Meyer, Nils and Rydzyk, Aljoscha and Pohnert, Georg}
}
@article {fenizia_cysteinolic_2021,
	title = {Cysteinolic Acid Is a Widely Distributed Compatible Solute of Marine Microalgae},
	journal = {Marine Drugs},
	volume = {19},
	number = {12},
	year = {2021},
	note = {Number: 12 Publisher: Multidisciplinary Digital Publishing Institute},
	month = {dec},
	pages = {683},
	abstract = {Phytoplankton rely on bioactive zwitterionic and highly polar small metabolites with osmoregulatory properties to compensate changes in the salinity of the surrounding seawater. Dimethylsulfoniopropionate (DMSP) is a main representative of this class of metabolites. Salinity-dependent DMSP biosynthesis and turnover contribute significantly to the global sulfur cycle. Using advanced chromatographic and mass spectrometric techniques that enable the detection of highly polar metabolites, we identified cysteinolic acid as an additional widely distributed polar metabolite in phytoplankton. Cysteinolic acid belongs to the class of marine sulfonates, metabolites that are commonly produced by algae and consumed by bacteria. It was detected in all dinoflagellates, haptophytes, diatoms and prymnesiophytes that were surveyed. We quantified the metabolite in different phytoplankton taxa and revealed that the cellular content can reach even higher concentrations than the ubiquitous DMSP. The cysteinolic acid concentration in the cells of the diatom Thalassiosira weissflogii increases significantly when grown in a medium with elevated salinity. In contrast to the compatible solute ectoine, cysteinolic acid is also found in high concentrations in axenic algae, indicating biosynthesis by the algae and not the associated bacteria. Therefore, we add this metabolite to the family of highly polar metabolites with osmoregulatory characteristics produced by phytoplankton.},
	keywords = {cysteinolic acid, diatoms, DMSP, ectoine, LC/MS analysis, osmoadaptation, osmoregulation, phytoplankton, RCC76, salinity},
	doi = {10.3390/md19120683},
	url = {https://www.mdpi.com/1660-3397/19/12/683},
	author = {Fenizia, Simona and Weissflog, Jerrit and Pohnert, Georg}
}
@article {Baumeister2020,
	title = {Identification to species level of live single microalgal cells from plankton samples with matrix-free laser/desorption ionization mass spectrometry},
	journal = {Metabolomics},
	volume = {16},
	number = {3},
	year = {2020},
	note = {ISBN: 0123456789 Publisher: Springer US tex.mendeley-tags: RCC 4667,RCC1717,RCC2561,RCC2562,RCC3008,RCC5791,RCC6807,RCC6808,RCC6809,RCC6810,RCC6811,RCC6812,RCC6813,RCC6814,RCC6815,RCC6816,RCC6817,RCC6818,RCC6819,RCC6820,RCC6821},
	month = {mar},
	pages = {28},
	keywords = {ionization high-, Live single-cell mass spectrometry, matrix-free laser desorption, Matrix-free laser desorption/ionization high-resol, Metabolic fingerprinting, Microalgal identification, RCC1717, RCC2561, RCC2562, RCC3008, RCC4667, RCC5791, RCC6807, RCC6808, RCC6809, RCC6810, RCC6811, RCC6812, RCC6813, RCC6814, RCC6815, RCC6816, RCC6817, RCC6818, RCC6819, RCC6820, RCC6821, resolution mass spectrometry, Spectral pattern matching, Spectrum similarity},
	issn = {1573-3882},
	doi = {10.1007/s11306-020-1646-7},
	url = {https://doi.org/10.1007/s11306-020-1646-7 http://link.springer.com/10.1007/s11306-020-1646-7},
	author = {Baumeister, Tim U H and Vallet, Marine and Kaftan, Filip and Guillou, Laure and Svato{\v s}, Ale{\v s} and Pohnert, Georg}
}
@article {Stettin2020,
	title = {Metabolomics benefits from orbitrap GC{\textendash}MS{\textemdash}Comparison of low- and high-resolution GC{\textendash}MS},
	journal = {Metabolites},
	volume = {10},
	number = {4},
	year = {2020},
	note = {tex.mendeley-tags: RCC75},
	month = {apr},
	pages = {143},
	abstract = {The development of improved mass spectrometers and supporting computational tools is expected to enable the rapid annotation of whole metabolomes. Essential for the progress is the identification of strengths and weaknesses of novel instrumentation in direct comparison to previous instruments. Orbitrap liquid chromatography (LC){\textendash}mass spectrometry (MS) technology is now widely in use, while Orbitrap gas chromatography (GC){\textendash}MS introduced in 2015 has remained fairly unexplored in its potential for metabolomics research. This study aims to evaluate the additional knowledge gained in a metabolomics experiment when using the high-resolution Orbitrap GC{\textendash}MS in comparison to a commonly used unit-mass resolution single-quadrupole GC{\textendash}MS. Samples from an osmotic stress treatment of a non-model organism, the microalga Skeletonema costatum, were investigated using comparative metabolomics with low- and high-resolution methods. Resulting datasets were compared on a statistical level and on the level of individual compound annotation. Both MS approaches resulted in successful classification of stressed vs. non-stressed microalgae but did so using different sets of significantly dysregulated metabolites. High-resolution data only slightly improved conventional library matching but enabled the correct annotation of an unknown. While computational support that utilizes high-resolution GC{\textendash}MS data is still underdeveloped, clear benefits in terms of sensitivity, metabolic coverage, and support in structure elucidation of the Orbitrap GC{\textendash}MS technology for metabolomics studies are shown here.},
	keywords = {Comparative metabolomics, Diatom, High-resolution mass spectrometry (HRMS), Instrument comparison, Mass Spectrometry (Orbitrap GC-MS), Metabolite identification, Orbitrap Gas Chromatography, Osmotic stress, RCC75},
	issn = {2218-1989},
	doi = {10.3390/metabo10040143},
	url = {https://www.mdpi.com/2218-1989/10/4/143},
	author = {Stettin, Daniel and Poulin, Remington X. and Pohnert, Georg}
}
@article {Gebser2020,
	title = {Phytoplankton-derived zwitterionic gonyol and dimethylsulfonioacetate interfere with microbial dimethylsulfoniopropionate sulfur cycling},
	journal = {MicrobiologyOpen},
	number = {February},
	year = {2020},
	note = {tex.mendeley-tags: RCC1731,RCC75,RCC76RCC1217,RCC841},
	month = {feb},
	pages = {e1014},
	keywords = {rcc1217, rcc1731, RCC75, RCC76, RCC841, school of life sciences, university of essex},
	issn = {20458827},
	doi = {10.1002/mbo3.1014},
	url = {http://doi.wiley.com/10.1002/mbo3.1014},
	author = {Gebser, Bj{\"o}rn and Thume, Kathleen and Steinke, Michael and Pohnert, Georg}
}
@article {Kuhlisch2017,
	title = {A fast and direct liquid chromatography-mass spectrometry method to detect and quantify polyunsaturated aldehydes and polar oxylipins in diatoms},
	journal = {Limnology and Oceanography: Methods},
	volume = {15},
	number = {1},
	year = {2017},
	note = {Publisher: John Wiley \& Sons, Ltd tex.mendeley-tags: RCC75,RCC776},
	month = {jan},
	pages = {70{\textendash}79},
	abstract = {Abstract Polyunsaturated aldehydes (PUAs) are a group of microalgal metabolites that have attracted a lot of attention due to their biological activity. Determination of PUAs has become an important routine procedure in plankton and biofilm investigations, especially those that deal with chemically mediated interactions. Here we introduce a fast and direct derivatization free method that allows quantifying PUAs in the nanomolar range, sufficient to undertake the analysis from cultures and field samples. The sample preparation requires one simple filtration step and the initiation of PUA formation by cell disruption. After centrifugation the samples are ready for measurement without any further handling. Within one chromatographic run this method additionally allows us to monitor the formation of the polar oxylipins arising from the cleavage of precursor fatty acids. The robust method is based on analyte separation and detection using ultra high performance liquid chromatography-atmospheric pressure chemical ionization mass spectrometry (UHPLC-APCI MS) and enables high throughput investigations by employing an analysis time of only 5 min. Our protocol thus provides an alternative and extension to existing PUA determinations based on gas chromatography-mass spectrometry (GC-MS) with shorter run times and without any chemical derivatization. It also enables researchers with widely available LC-MS analytical platforms to monitor PUAs. Additionally, non-volatile oxylipins such as ?-oxo-acids and related compounds can be elucidated and monitored.},
	keywords = {RCC75, RCC776},
	issn = {1541-5856},
	doi = {10.1002/lom3.10143},
	url = {https://doi.org/10.1002/lom3.10143},
	author = {Kuhlisch, Constanze and Deicke, Michael and Ueberschaar, Nico and Wichard, Thomas and Pohnert, Georg}
}
