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1. Additional file 2 of Water mass age structures the auxiliary metabolic gene content of free-living and particle-attached deep ocean viral communities

Author

Coutinho, Felipe H., Silveira, Cynthia B., Sebastián, Marta, Sánchez, Pablo, Duarte, Carlos M., Vaqué, Dolors, Gasol, Josep M., and Acinas, Silvia G.

Abstract

Additional file 2: Fig. S1. Relative abundance patterns of viral scaffolds encoding DHFR genes. A) Stacked bar plots depicting the RPKM abundances (y-axis) of viral scaffolds across samples (x-axis), separated by free-living and particle-attached samples (panels). Sampling stations are sorted from left to right by increasing oxygen concentrations. B) Box plots depicting the differences in DHFR encoding scaffold abundances between free-living and particle-attached fractions. Boxes depict the median, the first and third quartiles. Whiskers extend to 1.5 of the interquartile ranges. Outliers are represented as dots above or below whiskers. The p-values of each comparison obtained with the Mann-Whitney test are depicted above bars.

Published
2023
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2. Additional file 17 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Abstract

Additional file 17: Table S7. The 36 Malaspina stations (out of 120) featuring significant (p < 0.05) Local Contributions to Beta Diversity (LCBD) in prokaryotes and/or picoeukaryotes.

Published
2020
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3. Additional file 18 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Abstract

Additional file 18: Table S8.Malaspina eukaryotic and prokaryotic reads and OTUs-99% analysed during different steps of our in-house workflow.

Published
2020
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4. Additional file 20 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Abstract

Additional file 20: Figure S11. Same as Figure S10, Additional file 19 but using OTUs-ASVs. Solid and open squares indicate significant and nonsignificant (using p=0.05) correlations respectively between environmental similarity (in terms of temperature and fluorescence) and phylogenetic relatedness. Correlations that are significantly positive indicate that the phylogenetic distance between OTUs-ASVs increases as environmental similarity decreases for the phylogenetic range being analysed. Phylogenetic distances were measured as abundance-weighted β-Mean Nearest Taxon Distances (βMNTD).

Published
2020
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5. Additional file 19 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Abstract

Additional file 19: Figure S10. Phylogenetic signal was detected across short phylogenetic distances for both the 16S and 18S rRNA-gene markers as indicated by phylogenetic mantel correlograms (Malaspina dataset). Phylogenetic signal was tested using temperature and fluorescence, the two variables that explain the highest fraction of community variance. Solid and open squares indicate significant and nonsignificant (using p=0.05) correlations respectively between environmental similarity (in terms of temperature and fluorescence) and phylogenetic relatedness. Correlations that are significantly positive indicate that the phylogenetic distance between OTUs-99% increases as environmental similarity decreases for the phylogenetic range being analysed. Phylogenetic distances were measured as abundance-weighted β-Mean Nearest Taxon Distances (βMNTD).

Published
2020
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6. Additional file 9 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Abstract

Additional file 9: Figure S6. Species association networks for the tropical and subtropical surface-ocean microbiota as inferred from the Malaspina dataset. Left-hand side: Association networks of picoeukaryotes and prokaryotes considering positive (red) and negative (blue) correlations in panels A) [Eukaryotic Network (+-e)] and B) [Prokaryotic Network (+-e)], and only positive correlations in C) [Eukaryotic Network (+e)] and D) [Prokaryotic Network (+e)]. On the right-hand side, we present an alternative visualization of the network as well as the following network characteristics: number of nodes (n), number of edges with positive correlation (+e) and negative correlation (-e), average degree (avg. d), average path length (avg. l), global transitivity (t), number of modules with at least 3 nodes (m) and the number of nodes in each of those modules (sizes: n). The smaller network visualization on the right-hand side groups the nodes according to the modules. The colors of nodes in Left- and Right-hand side networks indicate the modules to which they belong (NB: colors in panels A, B, C & D are independent of each other).

Published
2020
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7. Additional file 6 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 6: Supplementary Methods.

8. Additional file 13 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 13: Figure S7. Percentage of OTUs-99% significantly associated to different environmental variables (MIC > 0.4) [left] and their corresponding contribution to total sequence abundance (i.e. percentage of reads) [right] in the Malaspina dataset. NB: Temperature, Oxygen, Conductivity and Salinity are correlated. OTUs can be associated to more than one variable.

9. Additional file 1 of Diversity and distribution of marine heterotrophic bacteria from a large culture collection

Author

Sanz-Sáez, Isabel, Salazar, Guillem, Sánchez, Pablo, Lara, Elena, Royo-Llonch, Marta, Sà, Elisabet L., Lucena, Teresa, Pujalte, María J., Vaqué, Dolors, Duarte, Carlos M., Gasol, Josep M., Pedrós-Alió, Carlos, Sánchez, Olga, and Acinas, Silvia G.

Subjects
14. Life underwater
Abstract

Additional file 1. Includes Supplementary Methods, Supplementary Figures and Supplementary Tables headings.

10. Additional file 11 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 11: Table S4. Summary of significant OTUs-99% associations using MIC for the Malaspina dataset.

11. Additional file 11 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 11: Table S4. Summary of significant OTUs-99% associations using MIC for the Malaspina dataset.

12. Additional file 16 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 16: Figure S9. Stations (total 36) from the Malaspina dataset featuring a comparatively large contribution to the overall β-diversity (LCBD = Local Contributions to Beta Diversity [38]; p

13. Additional file 14 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 14: Table S6. Significant MIC associations (MIC > 0.5) between OTUs and environmental parameters in the TARA Oceans dataset.

14. Additional file 1 of Diversity and distribution of marine heterotrophic bacteria from a large culture collection

Author

Sanz-Sáez, Isabel, Salazar, Guillem, Sánchez, Pablo, Lara, Elena, Royo-Llonch, Marta, Sà, Elisabet L., Lucena, Teresa, Pujalte, María J., Vaqué, Dolors, Duarte, Carlos M., Gasol, Josep M., Pedrós-Alió, Carlos, Sánchez, Olga, and Acinas, Silvia G.

Subjects
14. Life underwater
Abstract

Additional file 1. Includes Supplementary Methods, Supplementary Figures and Supplementary Tables headings.

15. Additional file 12 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 12: Table S5. Summary of significant OTUs-99% associations for the TARA Oceans dataset based on MIC.

16. Additional file 6 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 6: Supplementary Methods.

17. Additional file 10 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 10: Table S3. Summary of association networks from the Malaspina dataset based on SparCC.

18. Additional file 14 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 14: Table S6. Significant MIC associations (MIC > 0.5) between OTUs and environmental parameters in the TARA Oceans dataset.

19. Additional file 3 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 3: Table S1. Regionally abundant or rare prokaryotic and picoeukaryotic OTUs-99% from the Malaspina dataset.

20. Additional file 5 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 5: Table S2. OTUs-99% displaying Cosmopolitan, Intermediate and Restricted distributions in the Malaspina dataset.

21. Additional file 12 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 12: Table S5. Summary of significant OTUs-99% associations for the TARA Oceans dataset based on MIC.

22. Additional file 8 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 8: Figure S5. Percentage of variance in Picoeukaryotic and Prokaryotic community composition (ADONIS R2) explained by water temperature and fluorescence when using different β-diversity metrics. Figure based on the Malaspina Meta-57 dataset.

23. Additional file 7 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 7: Figure S4. The 57 Malaspina stations for which 17 environmental parameters were available (Meta-57 dataset).

24. Additional file 2 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 2: Figure S2. Bray Curtis and gUniFrac distances between picoeukaryotes and prokaryotes from the Malaspina dataset. Regression (blue) and 0:1 (red) lines are indicated.

25. Additional file 8 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 8: Figure S5. Percentage of variance in Picoeukaryotic and Prokaryotic community composition (ADONIS R2) explained by water temperature and fluorescence when using different β-diversity metrics. Figure based on the Malaspina Meta-57 dataset.

26. Additional file 2 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 2: Figure S2. Bray Curtis and gUniFrac distances between picoeukaryotes and prokaryotes from the Malaspina dataset. Regression (blue) and 0:1 (red) lines are indicated.

27. Additional file 10 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 10: Table S3. Summary of association networks from the Malaspina dataset based on SparCC.

28. Additional file 3 of Disentangling the mechanisms shaping the surface ocean microbiota

Author

Logares, Ramiro, Deutschmann, Ina M., Junger, Pedro C., Giner, Caterina R., Krabberød, Anders K., Schmidt, Thomas S. B., Rubinat-Ripoll, Laura, Mestre, Mireia, Salazar, Guillem, Ruiz-González, Clara, Sebastián, Marta, Colomban De Vargas, Acinas, Silvia G., Duarte, Carlos M., Gasol, Josep M., and Massana, Ramon

Subjects
14. Life underwater
Abstract

Additional file 3: Table S1. Regionally abundant or rare prokaryotic and picoeukaryotic OTUs-99% from the Malaspina dataset.

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