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opencc-by-4.0Nov 2023View details →

Analysis of Metabolomics Data to Assess Interactions in Microalgal Co-culture of Skeletonema marinoi and Prymnesium parvum

This dataset refers to the metabolomics results from Metabolome Annotation QWorkflow on a co-culture of two microalgae: Skeletonema marinoi and Prymnesium parvum. The metabolomics data was acquired from endometabolome and exometabolome in both positive and negative MS modes. These will be referred as conditions. The files ms2_spectra_condition.mzML files have the MS2 combined from different MS2 files found on Zenodo with DOI: 10.5281/zenodo.10143233. The MS1 files are available on Zenodo as well with the DOI: 10.5281/zenodo.10143127 The first section is about the results from the MS1 analysis. For the code used to generate these files, please refer to the code: <a href="https://github.com/zmahnoor14/MAW/tree/main/co-culture">https://github.com/zmahnoor14/MAW/tree/main/co-culture</a>  <ol> <li>Feature_info_condition.csv refers to the list of features with IDS, m/z, rt and intensity values. <ul> <li>The feature list is used to link the MS1 features to the features extracted from MS2 spectra.</li> </ul> </li> <li>Feature_list_condition.csv refers to the list of mzML origin file (samples) and the intensity of the features in those samples.</li> </ol> The second section relates to the MS2 results. For source code please refer to: <a href="https://github.com/zmahnoor14/MAW/tree/main/Docker">https://github.com/zmahnoor14/MAW/tree/main/Docker</a> <ol> <li>SL_MAW_Coculture.csv contains list of metabolic features that were annotated and found to be present in the suspect list of either of the two organisms or both. The suspect lists for Skeletonema marinoi can be found at 10.5281/zenodo.5772755, and for Prymnesium parvum can be found at 10.5281/zenodo.7864506.  </li> <li>unique_MAW_SMILES_coculture.csv file contains all information on unique SMILES.</li> <li>onlyDAF.csv contains differentially abundant features in either of the conditions: S. marinoi co-culture, S. marinoi mono-culture and similar conditions for P. parvum.</li> <li>condition_mergedResults-with-one-Candidates_sig_feat_for_only_inclusion.csv files contain all MS2 features and annotations together with the information on whether these features were found in the inclusion list (List provided for generating MS2 spectra in orbitrap), and whether these features were differential.</li> </ol>

opencc-by-4.0Jan 2024View details →

Tandem Mass Spectrometry Data (LCMS-2) from Microalgal Co-culture of Skeletonema marinoi and Prymnesium parvum

The mzML files in this dataset are the Liquid Chromatography Tandem Mass Spectrometry (LCMS-2) data files, derived from the RAW MS-2 files using GNPS file convertor. These files contain unprocessed features fragmented features from the MS-1 data files available as <10.5281/zenodo.10143127> acquired from the monocultures (single species: Skeletonema marinoi and Prymnesium parvum separately) and co-culture conditions of (Skeletonema marinoi and Prymnesium parvum). These files are used for structure annotations.  The results of metabolomics annotation are available on Zenodo with DOI: 10.5281/zenodo.10143554

opencc-by-4.0Jan 2024View details →

Liquid Chromatography Mass Spectrometry Data (LCMS-1) from Microalgal Co-culture of Skeletonema marinoi and Prymnesium parvum

The mzML files in this dataset are the Liquid Chromatography Mass Spectrometry Data (LCMS-1) data files, derived from the RAW MS files using GNPS file convertor. These files contain unprocessed features acquired from the monocultures (single species: Skeletonema marinoi and Prymnesium parvum separately) and co-culture conditions of (Skeletonema marinoi and Prymnesium parvum). The microalgae were grown in co-culture chambers, so the naming convention A, and B refer to the two sides of the chamber. So, 1a and 1b are S. marinoi monocultures, but 11a and 11b refer to s. marinoi and P. parvum respectively. The results of metabolomics data analysis are available on Zenodo with DOI: 10.5281/zenodo.10143554

opencc-by-4.0Dec 2023View details →

Transcriptome Analysis from a co-culture of Skeletonema marinoi and Prymnesium parvum

This Zenodo entry refers to a study using metabolomics and transcriptomic data analysis to analyse chemical interactions between two microalgae: Skeletonema marinoi and Prymnesium parvum p_parvum_Eukaryota_augustus_gene_prediction.faa file contains the predicted protein sequences from the transcriptome of Prymnesium parvum using Augustus. This list is generated from a non-restrictive Busco Analysis. s_costatum_Stramenopiles_augustus_gene_prediction.faa file contains the predicted protein sequences from the transcriptome of Skeletonema marinoi using Augustus. This list is generated from a restrictive Busco Analysis. The files p_parvum_deseq2_results_all.csv and s_marinoi_deseq2_results_all.csv contain differential gene expression analysis, while p_parvum_deseq2_result_sorted_regulated_with_proteins.csv and s_marinoi_deseq2_result_sorted_regulated_with_proteins.csv contain only upregulated protein sequences in co-culture conditions. The genes_read.R script is used to generate the p_parvum_deseq2_result_sorted_regulated_with_proteins.csv and s_marinoi_deseq2_result_sorted_regulated_with_proteins.csv. The code for analysis from RAW reads to differential gene expression analysis is available on: <a href="https://github.com/Bioinformatics-Core-Facility-Jena/SE20220705_97">https://github.com/Bioinformatics-Core-Facility-Jena/SE20220705_97</a>. The RAW files are available on BioProject: PRJNA1006530

opencc-by-4.0Jan 2023View details →

Skeletonema marinoi MS2 mzML files in negative mode

These are MS2 files in .mzML format acquired in negative mode. The extracted metabolites come from a sample from Skeletonema marinoi.

opencc-by-4.0Apr 2023View details →

Results from MAW - Skeletonema marinoi

This dataset contains a list of metabolites annotated from the Mass Spectrometry data from Skeletonema marinoi.  1. The csv file "all_features_candidates_withNamesAndSource.csv" is a list of annotated metabolites obtained from the whole metabolome annotation of S. marinoi using Metabolome Annotation workflow (MAW). (corresponding Sunburst is Smarinoi_sunburst.html) 2. The csv file "intersection.csv" contains metabolites common in the "all_features_candidates_withNamesAndSource.csv" and the suspect list of the S. marinoi with Zenodo DOI: 10.5281/zenodo.5772755. (corresponding Sunburst is intersection_sunburst.html) 3. The csv file "SmarinoiUnion.csv" is a union set from Suspect list Zenodo (DOI: 10.5281/zenodo.5772755) and "all_features_candidates_withNames.csv". (corresponding Sunburst is union_sunburst.html) 4. only_MAW_curated.csv contains previously not known compounds from S. marinoi 5. insection_sl_sm_sunburst.html is the sunburst from intersection.csv.

dryad36/100

Adaptive phenotypic evolution of Skeletonema costatum to ocean acidification and warming with trade-offs from a multi-year outdoor experiment

Open the record for dataset details and reuse information.

publicJul 2025View details →

opencc-by-4.0Jun 2024View details →

Unveiling the Influence of Light Intensity on Fucoxanthin Synthesis in Skeletonema Costatum

This material has presented on 2nd International Conference on Advanced Research in Engineering and Technology in October 25, 2023.

dryad32/100

Local adaptation through countergradient selection in northern populations of Skeletonema marinoi

Marine microorganisms have the potential to disperse widely with few obvious barriers to gene flow. However, among microalgae, several studies have demonstrated that species can be highly genetically structured with limited gene flow among populations, despite hydrographic connectivity. Ecological differentiation and local adaptation have been suggested as drivers of such population structure. Here we tested whether multiple strains from two genetically distinct Baltic Sea populations of the diatom Skeletonema marinoi showed evidence of local adaptation to their local environments; the estuarine Bothnian Sea and the marine Kattegat Sea. We performed reciprocal transplants of multiple strains between culture media based on water from the respective environments, and we also allowed competition between strains of estuarine and marine origin in both salinities. When grown alone, both marine and estuarine strains performed best in the high salinity environment, and estuarine strains always grew faster than marine strains. This result suggests local adaptation through countergradient selection, i.e. genetic effects counteract environmental effects. However, higher growth rate of the estuarine strains appears to have a cost in the marine environment and when strains were allowed to compete, marine strains performed better than estuarine strains in the marine environment. Thus, other traits are likely to also affect fitness. We provide evidence that tolerance to pH could be involved, and that estuarine strains which are adapted to a more fluctuating pH continue growing at higher pH than marine strains.

opencc-zeroOct 2022View details →

FIGURE 29 in Further studies on the species diversity of the marine planktonic diatom genus Skeletonema (Bacillariophyta) in the Mexican Pacific

FIGURE 29. Violin plot with cell diameter of the four species studied, based on the data of Table 1.

FIGURES 7–11 in Further studies on the species diversity of the marine planktonic diatom genus Skeletonema (Bacillariophyta) in the Mexican Pacific

FIGURES 7–11. Skeletonema ardens, SEM (7, 9) and TEM (8, 10, 11). Fig. 7. A complete frustule in a chain, showing high mantle with tiny spines or knobs (small arrows), intercalary and terminal fulto- and rimoportulae (TR with an arrow), and 1:1 junctions of IF. Fig. 8. Terminal valve with high mantle bearing tiny spines or knobs (small arrows), fultoportulae (perhaps broken), a rather short rimoportula (arrow), and parts of the valvocopula and copulae. Fig. 9. Two terminal cells in division showing the IF's and the long IR's, almost touching each other (arrow). Fig. 10. Detail of TF's and TR (arrows), note the very spiny tips of the TF's. Fig. 11. Detail of a terminal truncated fultoportula showing three satellite pores at its base (arrow).

FIGURES 1–6 in Further studies on the species diversity of the marine planktonic diatom genus Skeletonema (Bacillariophyta) in the Mexican Pacific

FIGURES 1–6. Skeletonema ardens, LM (1–3), SEM (4, 5) and TEM (6). Figs 1–3. Three different chains with 2, 5 and 6 cells, respectively, with one to two chloroplasts per cell; the small arrow (Fig. 1) points to a long terminal process (probably a rimoportula). Fig. 4. A short chain with two cells, arrows point to terminal rimoportulae (TR's). Fig. 5. Solitary cell with very long fulto- and rimoportulae (arrows). Fig. 6. Chain with three cells, showing the terminal fulto- and the single rimoportula (arrow).

FIGURES 23–28 in Further studies on the species diversity of the marine planktonic diatom genus Skeletonema (Bacillariophyta) in the Mexican Pacific

FIGURES 23–28. Skeletonema tropicum, LM (23) and SEM (24–28). Fig. 23. A long and robust chain with 12 cells, some cells dividing and each cell with 4–6 chloroplasts. Fig. 24. Terminal part of a chain, with developing or collapsed TF's and TR, and very short IR's (small arrows). Fig. 25. A complete chain (6 cells), most probably developing, with overlaid copulae between various intercalary valves. Fig. 26. Intercalary cells and valves with IF's fusing in 1:1 and 1:2 types; delicate and thin threads of unknown nature are coming out from some IF's (small arrows). Fig. 27. Terminal cell and valve showing the areolae on the face and mantle, mantle also shows very delicate siliceous ridges, the TF's have clawlike tips or tips with fine spines, and a single, long TR (arrow). Fig. 28. Internal view of a valve with details of the areolation, the fultoportulae (with three satellite pores), and a single labiate structure of the rimoportula (arrow).

FIGURES 18–22 in Further studies on the species diversity of the marine planktonic diatom genus Skeletonema (Bacillariophyta) in the Mexican Pacific

FIGURES 18–22. Skeletonema pseudocostatum, LM (18) and SEM (19–22). Fig. 18. A complete chain with 9 cells, one cell is dividing (arrow). Fig. 19. Broken chain with 4 cells in development. Fig. 20. Terminal part of a chain, with fusion of the IF's, including 1:1 and 1:2 junctions. Fig. 21. Two terminal valves with relative high valve mantle and TF's showing the characteristic spines of their tips (small arrows) and a TR (arrow). Fig. 22. A terminal valve showing the areolae on the face, TF's and TR (arrow).

FIGURES 12–17 in Further studies on the species diversity of the marine planktonic diatom genus Skeletonema (Bacillariophyta) in the Mexican Pacific

FIGURES 12–17. Skeletonema grevillei, LM (12), SEM (13–16) and TEM (17). Fig. 12. A rather long chain of 8 cells, some of them dividing, containing two chloroplasts per cell. Fig. 13. Terminal part of a chain showing terminal and intercalary valves, siliceous ridges (small arrows) between face and mantle at the terminal valve, TF's, one TR (arrow), and broken IF's. Fig. 14. Intercalary valves with IF's fusing to those of sibling valve in 1:1 junction type, a short IR (arrow), and siliceous ridges (small arrows) around bases of IF's. Fig. 15. Terminal valve with fultoportulae (TF's) irregularly truncated, a marginal rimoportula (arrow), and siliceous ridges (small arrows) dividing valve face and mantle. Fig. 16. Another terminal valve showing details of the areolae, siliceous ridges (small arrows) around bases of the TF's, and a marginal rimoportula with slightly inflated tip (arrow). Fig. 17. Details of the three to four satellite pores surrounding each fultoportula (arrows).