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1. Alpha-glucans from bacterial necromass indicate an intra-population loop within the marine carbon cycle

Author

Beidler, Irena, Steinke, Nicola, Schulze, Tim, Sidhu, Chandni, Bartosik, Daniel, Zühlke, Marie-Katherin, Martin, Laura Torres, Krull, Joris, Dutschei, Theresa, Ferrero-Bordera, Borja, Rielicke, Julia, Kale, Vaikhari, Sura, Thomas, Trautwein-Schult, Anke, Kirstein, Inga V., Wiltshire, Karen H., Teeling, Hanno, Becher, Dörte, Bengtsson, Mia Maria, Hehemann, Jan-Hendrik, Bornscheuer, Uwe. T., Amann, Rudolf I., and Schweder, Thomas

Published
2024
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3. Thousands of small, novel genes predicted in global phage genomes

Author

Fremin, Brayon J, Bhatt, Ami S, Kyrpides, Nikos C, Consortium, Global Phage Small Open Reading Frame, Sengupta, Aditi, Sczyrba, Alexander, da Silva, Aline Maria, Buchan, Alison, Gaudin, Amelie, Brune, Andreas, Hirsch, Ann M, Neumann, Anthony, Shade, Ashley, Visel, Axel, Campbell, Barbara, Baker, Brett, Hedlund, Brian P, Crump, Byron C, Currie, Cameron, Kelly, Charlene, Craft, Chris, Hazard, Christina, Francis, Christopher, Schadt, Christopher W, Averill, Colin, Mobilian, Courtney, Buckley, Dan, Hunt, Dana, Noguera, Daniel, Beck, David, Valentine, David L, Walsh, David, Sumner, Dawn, Lymperopoulou, Despoina, Bhaya, Devaki, Bryant, Donald A, Morrison, Elise, Brodie, Eoin, Young, Erica, Lilleskov, Erik, Högfors-Rönnholm, Eva, Chen, Feng, Stewart, Frank, Nicol, Graeme W, Teeling, Hanno, Beller, Harry R, Dionisi, Hebe, Liao, Hui-Ling, Beman, J Michael, Stegen, James, Tiedje, James, Jansson, Janet, VanderGheynst, Jean, Norton, Jeanette, Dangl, Jeff, Blanchard, Jeffrey, Bowen, Jennifer, Macalady, Jennifer, Pett-Ridge, Jennifer, Rich, Jeremy, Payet, Jérôme P, Gladden, John D, Raff, Jonathan D, Klassen, Jonathan L, Tarn, Jonathan, Neufeld, Josh, Gravuer, Kelly, Hofmockel, Kirsten, Chen, Ko-Hsuan, Konstantinidis, Konstantinos, DeAngelis, Kristen M, Partida-Martinez, Laila P, Meredith, Laura, Chistoserdova, Ludmila, Moran, Mary Ann, Scarborough, Matthew, Schrenk, Matthew, Sullivan, Matthew, David, Maude, O'Malley, Michelle A, Medina, Monica, Habteselassie, Mussie, Ward, Nicholas D, Pietrasiak, Nicole, Mason, Olivia U, Sorensen, Patrick O, de los Santos, Paulina Estrada, Baldrian, Petr, McKay, R Michael, Simister, Rachel, Stepanauskas, Ramunas, Neumann, Rebecca, Malmstrom, Rex, Cavicchioli, Ricardo, Kelly, Robert, Hatzenpichler, Roland, Stocker, Roman, Cattolico, Rose Ann, Ziels, Ryan, and Vilgalys, Rytas

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, 2.1 Biological and endogenous factors, Generic health relevance, Bacteriophages, Genome, Viral, Genomics, Microbiota, Phylogeny, Global Phage Small Open Reading Frame (GP-SmORF) Consortium, CP: Microbiology, MetaRibo-Seq, comparative genomics, gene families, microbiome, phage, sORFs, small genes, Biochemistry and Cell Biology, Medical Physiology, Biological sciences
Abstract

Small genes (40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.

Published
2022

6. Thousands of small, novel genes predicted in global phage genomes

Author

Sengupta, Aditi, Sczyrba, Alexander, Maria da Silva, Aline, Buchan, Alison, Gaudin, Amelie, Brune, Andreas, Hirsch, Ann M., Neumann, Anthony, Shade, Ashley, Visel, Axel, Campbell, Barbara, Baker, Brett, Hedlund, Brian P., Crump, Byron C., Currie, Cameron, Kelly, Charlene, Craft, Chris, Hazard, Christina, Francis, Christopher, Schadt, Christopher W., Averill, Colin, Mobilian, Courtney, Buckley, Dan, Hunt, Dana, Noguera, Daniel, Beck, David, Valentine, David L., Walsh, David, Sumner, Dawn, Lymperopoulou, Despoina, Bhaya, Devaki, Bryant, Donald A., Morrison, Elise, Brodie, Eoin, Young, Erica, Lilleskov, Erik, Högfors-Rönnholm, Eva, Chen, Feng, Stewart, Frank, Nicol, Graeme W., Teeling, Hanno, Beller, Harry R., Dionisi, Hebe, Liao, Hui-Ling, Beman, J. Michael, Stegen, James, Tiedje, James, Jansson, Janet, VanderGheynst, Jean, Norton, Jeanette, Dangl, Jeff, Blanchard, Jeffrey, Bowen, Jennifer, Macalady, Jennifer, Pett-Ridge, Jennifer, Rich, Jeremy, Payet, Jérôme P., Gladden, John D., Raff, Jonathan D., Klassen, Jonathan L., Tarn, Jonathan, Neufeld, Josh, Gravuer, Kelly, Hofmockel, Kirsten, Chen, Ko-Hsuan, Konstantinidis, Konstantinos, DeAngelis, Kristen M., Partida-Martinez, Laila P., Meredith, Laura, Chistoserdova, Ludmila, Moran, Mary Ann, Scarborough, Matthew, Schrenk, Matthew, Sullivan, Matthew, David, Maude, O'Malley, Michelle A., Medina, Monica, Habteselassie, Mussie, Ward, Nicholas D., Pietrasiak, Nicole, Mason, Olivia U., Sorensen, Patrick O., Estrada de los Santos, Paulina, Baldrian, Petr, McKay, R. Michael, Simister, Rachel, Stepanauskas, Ramunas, Neumann, Rebecca, Malmstrom, Rex, Cavicchioli, Ricardo, Kelly, Robert, Hatzenpichler, Roland, Stocker, Roman, Cattolico, Rose Ann, Ziels, Ryan, Vilgalys, Rytas, Blumer-Schuette, Sara, Crowe, Sean, Roux, Simon, Hallam, Steven, Lindow, Steven, Brawley, Susan H., Tringe, Susannah, Woyke, Tanja, Whitman, Thea, Bianchi, Thomas, Mock, Thomas, Donohue, Timothy, James, Timothy Y., Kalluri, Udaya C., Karaoz, Ulas, Denef, Vincent, Liu, Wen-Tso, Whitman, William, Ouyang, Yang, Fremin, Brayon J., Bhatt, Ami S., and Kyrpides, Nikos C.

Published
2022
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13. Marine particle microbiomes during a spring diatom bloom contain active sulfate-reducing bacteria.

Author

Siebers, Robin, Schultz, Doreen, Farza, Mohamed S, Brauer, Anne, Zühlke, Daniela, Mücke, Pierre A, Wang, Fengqing, Bernhardt, Jörg, Teeling, Hanno, Becher, Dörte, Riedel, Katharina, Kirstein, Inga V, Wiltshire, Karen H, Hoff, Katharina J, Schweder, Thomas, Urich, Tim, and Bengtsson, Mia M

Subjects
SULFATE-reducing bacteria, SPRING, ALGAL blooms, PHYTOPLANKTON, ALGAL cells, CARBON sequestration, PHAEODACTYLUM tricornutum, DIATOMS
Abstract

Phytoplankton blooms fuel marine food webs with labile dissolved carbon and also lead to the formation of particulate organic matter composed of living and dead algal cells. These particles contribute to carbon sequestration and are sites of intense algal-bacterial interactions, providing diverse niches for microbes to thrive. We analyzed 16S and 18S ribosomal RNA gene amplicon sequences obtained from 51 time points and metaproteomes from 3 time points during a spring phytoplankton bloom in a shallow location (6-10 m depth) in the North Sea. Particulate fractions larger than 10 µm diameter were collected at near daily intervals between early March and late May in 2018. Network analysis identified two major modules representing bacteria co-occurring with diatoms and with dinoflagellates, respectively. The diatom network module included known sulfate-reducing Desulfobacterota as well as potentially sulfur-oxidizing Ectothiorhodospiraceae. Metaproteome analyses confirmed presence of key enzymes involved in dissimilatory sulfate reduction, a process known to occur in sinking particles at greater depths and in sediments. Our results indicate the presence of sufficiently anoxic niches in the particle fraction of an active phytoplankton bloom to sustain sulfate reduction, and an important role of benthic-pelagic coupling for microbiomes in shallow environments. Our findings may have implications for the understanding of algal-bacterial interactions and carbon export during blooms in shallow-water coastal areas. [ABSTRACT FROM AUTHOR]

Published
2024
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14. Unveiling the role of novel carbohydrate‐binding modules in laminarin interaction of multimodular proteins from marine Bacteroidota during phytoplankton blooms.

Author

Zühlke, Marie‐Katherin, Ficko‐Blean, Elizabeth, Bartosik, Daniel, Terrapon, Nicolas, Jeudy, Alexandra, Jam, Murielle, Wang, Fengqing, Welsch, Norma, Dürwald, Alexandra, Martin, Laura Torres, Larocque, Robert, Jouanneau, Diane, Eisenack, Tom, Thomas, François, Trautwein‐Schult, Anke, Teeling, Hanno, Becher, Dörte, Schweder, Thomas, and Czjzek, Mirjam

Subjects
ALGAL blooms, PROTEIN-protein interactions, MARINE bacteria, PHAEODACTYLUM tricornutum, BACTERIAL cell surfaces, BACTERIAL genomes, PHYTOPLANKTON
Abstract

Laminarin, a β(1,3)‐glucan, serves as a storage polysaccharide in marine microalgae such as diatoms. Its abundance, water solubility and simple structure make it an appealing substrate for marine bacteria. Consequently, many marine bacteria have evolved strategies to scavenge and decompose laminarin, employing carbohydrate‐binding modules (CBMs) as crucial components. In this study, we characterized two previously unassigned domains as laminarin‐binding CBMs in multimodular proteins from the marine bacterium Christiangramia forsetii KT0803T, thereby introducing the new laminarin‐binding CBM families CBM102 and CBM103. We identified four CBM102s in a surface glycan‐binding protein (SGBP) and a single CBM103 linked to a glycoside hydrolase module from family 16 (GH16_3). Our analysis revealed that both modular proteins have an elongated shape, with GH16_3 exhibiting greater flexibility than SGBP. This flexibility may aid in the recognition and/or degradation of laminarin, while the constraints in SGBP could facilitate the docking of laminarin onto the bacterial surface. Exploration of bacterial metagenome‐assembled genomes (MAGs) from phytoplankton blooms in the North Sea showed that both laminarin‐binding CBM families are widespread among marine Bacteroidota. The high protein abundance of CBM102‐ and CBM103‐containing proteins during phytoplankton blooms further emphasizes their significance in marine laminarin utilization. [ABSTRACT FROM AUTHOR]

Published
2024
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15. Symbiosis insights through metagenomic analysis of a microbial consortium

Author

Woyke, Tanja, Teeling, Hanno, Ivanova, Natalia N., Hunteman, Marcel, Richter, Michael, Gloeckner, Frank Oliver, Boffelli, Dario, Barry, Kerrie W., Shapiro, Harris J., Anderson, Iain J., Szeto, Ernest, Kyrpides, Nikos C., Mussmann, Marc, Amann, Rudolf, Bergin, Claudia, Ruehland, Caroline, Rubin, Edward M., and Dubilier, Nicole

Subjects
Basic biological sciences
Published
2006

17. Adaptive mechanisms that provide competitive advantages to marine bacteroidetes during microalgal blooms

Author

Unfried, Frank, Becker, Stefan, Robb, Craig S., Hehemann, Jan-Hendrik, Markert, Stephanie, Heiden, Stefan E., Hinzke, Tjorven, Becher, Dörte, Reintjes, Greta, Krüger, Karen, Avcı, Burak, Kappelmann, Lennart, Hahnke, Richard L., Fischer, Tanja, Harder, Jens, Teeling, Hanno, Fuchs, Bernhard, Barbeyron, Tristan, Amann, Rudolf I., and Schweder, Thomas

Published
2018
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18. Alpha-glucans from bacterial necromass indicate an intra-population loop within the marine carbon cycle

Author

Schweder, Thomas, primary, Beidler, Irena, additional, Steinke, Nicola, additional, Schulze, Tim, additional, Sidhu, Chandni, additional, Bartosik, Daniel, additional, Krull, Joris, additional, Dutschei, Theresa, additional, Ferrero-Bordera, Borja, additional, Rielicke, Julia, additional, Kale, Vaikhari, additional, Sura, Thomas, additional, Trautwein-Schult, Anke, additional, Kirstein, Inga, additional, Wiltshire, Karen, additional, Teeling, Hanno, additional, Becher, Dörte, additional, Bengtsson, Mia, additional, Hehemann, Jan-Hendrik, additional, Bornscheuer, Uwe, additional, and Amann, Rudolf, additional

Published
2023
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19. Unraveling the functional dark matter through global metagenomics

Author

Pavlopoulos, Georgios A., Baltoumas, Fotis A., Liu, Sirui, Selvitopi, Oguz, Camargo, Antonio Pedro, Nayfach, Stephen, Azad, Ariful, Roux, Simon, Call, Lee, Ivanova, Natalia N., Chen, I. Min, Paez-Espino, David, Karatzas, Evangelos, Acinas, Silvia G., Ahlgren, Nathan, Attwood, Graeme, Baldrian, Petr, Berry, Timothy, Bhatnagar, Jennifer M., Bhaya, Devaki, Bidle, Kay D., Blanchard, Jeffrey L., Boyd, Eric S., Bowen, Jennifer L., Bowman, Jeff, Brawley, Susan H., Brodie, Eoin L., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Cadillo-Quiroz, Hinsby, Campbell, Barbara J., Cavicchioli, Ricardo, Chuckran, Peter F., Coleman, Maureen, Crowe, Sean, Colman, Daniel R., Currie, Cameron R., Dangl, Jeff, Delherbe, Nathalie, Denef, Vincent J., Dijkstra, Paul, Distel, Daniel D., Eloe-Fadrosh, Emiley, Fisher, Kirsten, Francis, Christopher, Garoutte, Aaron, Gaudin, Amelie, Gerwick, Lena, Godoy-Vitorino, Filipa, Guerra, Peter, Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hentschel, Ute, Hess, Matthias, Hirsch, Ann M., Hug, Laura A., Hultman, Jenni, Hunt, Dana E., Huntemann, Marcel, Inskeep, William P., James, Timothy Y., Jansson, Janet, Johnston, Eric R., Kalyuzhnaya, Marina, Kelly, Charlene N., Kelly, Robert M., Klassen, Jonathan L., Nüsslein, Klaus, Kostka, Joel E., Lindow, Steven, Lilleskov, Erik, Lynes, Mackenzie, Mackelprang, Rachel, Martin, Francis M., Mason, Olivia U., McKay, R. Michael, McMahon, Katherine, Mead, David A., Medina, Monica, Meredith, Laura K., Mock, Thomas, Mohn, William W., Moran, Mary Ann, Murray, Alison, Neufeld, Josh D., Neumann, Rebecca, Norton, Jeanette M., Partida-Martinez, Laila P., Pietrasiak, Nicole, Pelletier, Dale, Reddy, T. B. K., Reese, Brandi Kiel, Reichart, Nicholas J., Reiss, Rebecca, Saito, Mak A., Schachtman, Daniel P., Seshadri, Rekha, Shade, Ashley, Sherman, David, Simister, Rachel, Simon, Holly, Stegen, James, Stepanauskas, Ramunas, Sullivan, Matthew, Sumner, Dawn Y., Teeling, Hanno, Thamatrakoln, Kimberlee, Treseder, Kathleen, Tringe, Susannah, Vaishampayan, Parag, Valentine, David L., Waldo, Nicholas B., Waldrop, Mark P., Walsh, David A., Ward, David M., Wilkins, Michael, Whitman, Thea, Woolet, Jamie, Woyke, Tanja, Iliopoulos, Ioannis, Konstantinidis, Konstantinos, Tiedje, James M., Pett-Ridge, Jennifer, Baker, David, Visel, Axel, Ouzounis, Christos A., Ovchinnikov, Sergey, Buluç, Aydin, Kyrpides, Nikos C., Pavlopoulos, Georgios A., Baltoumas, Fotis A., Liu, Sirui, Selvitopi, Oguz, Camargo, Antonio Pedro, Nayfach, Stephen, Azad, Ariful, Roux, Simon, Call, Lee, Ivanova, Natalia N., Chen, I. Min, Paez-Espino, David, Karatzas, Evangelos, Acinas, Silvia G., Ahlgren, Nathan, Attwood, Graeme, Baldrian, Petr, Berry, Timothy, Bhatnagar, Jennifer M., Bhaya, Devaki, Bidle, Kay D., Blanchard, Jeffrey L., Boyd, Eric S., Bowen, Jennifer L., Bowman, Jeff, Brawley, Susan H., Brodie, Eoin L., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Cadillo-Quiroz, Hinsby, Campbell, Barbara J., Cavicchioli, Ricardo, Chuckran, Peter F., Coleman, Maureen, Crowe, Sean, Colman, Daniel R., Currie, Cameron R., Dangl, Jeff, Delherbe, Nathalie, Denef, Vincent J., Dijkstra, Paul, Distel, Daniel D., Eloe-Fadrosh, Emiley, Fisher, Kirsten, Francis, Christopher, Garoutte, Aaron, Gaudin, Amelie, Gerwick, Lena, Godoy-Vitorino, Filipa, Guerra, Peter, Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hentschel, Ute, Hess, Matthias, Hirsch, Ann M., Hug, Laura A., Hultman, Jenni, Hunt, Dana E., Huntemann, Marcel, Inskeep, William P., James, Timothy Y., Jansson, Janet, Johnston, Eric R., Kalyuzhnaya, Marina, Kelly, Charlene N., Kelly, Robert M., Klassen, Jonathan L., Nüsslein, Klaus, Kostka, Joel E., Lindow, Steven, Lilleskov, Erik, Lynes, Mackenzie, Mackelprang, Rachel, Martin, Francis M., Mason, Olivia U., McKay, R. Michael, McMahon, Katherine, Mead, David A., Medina, Monica, Meredith, Laura K., Mock, Thomas, Mohn, William W., Moran, Mary Ann, Murray, Alison, Neufeld, Josh D., Neumann, Rebecca, Norton, Jeanette M., Partida-Martinez, Laila P., Pietrasiak, Nicole, Pelletier, Dale, Reddy, T. B. K., Reese, Brandi Kiel, Reichart, Nicholas J., Reiss, Rebecca, Saito, Mak A., Schachtman, Daniel P., Seshadri, Rekha, Shade, Ashley, Sherman, David, Simister, Rachel, Simon, Holly, Stegen, James, Stepanauskas, Ramunas, Sullivan, Matthew, Sumner, Dawn Y., Teeling, Hanno, Thamatrakoln, Kimberlee, Treseder, Kathleen, Tringe, Susannah, Vaishampayan, Parag, Valentine, David L., Waldo, Nicholas B., Waldrop, Mark P., Walsh, David A., Ward, David M., Wilkins, Michael, Whitman, Thea, Woolet, Jamie, Woyke, Tanja, Iliopoulos, Ioannis, Konstantinidis, Konstantinos, Tiedje, James M., Pett-Ridge, Jennifer, Baker, David, Visel, Axel, Ouzounis, Christos A., Ovchinnikov, Sergey, Buluç, Aydin, and Kyrpides, Nikos C.

Abstract

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.

Published
2023
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21. Additional file 2 of Epiphytic common core bacteria in the microbiomes of co-located green (Ulva), brown (Saccharina) and red (Grateloupia, Gelidium) macroalgae

Author

Lu, De-Chen, Wang, Feng-Qing, Amann, Rudolf I., Teeling, Hanno, and Du, Zong-Jun

Abstract

Additional file 2: Compilation of supplementary figures. Figure S1. a) Diversities of macroalgae, seawater and sediment samples as assessed by Shannon and Simpson indices as well as Good’s coverage of 16S rRNA ASVs. Statistical significance was assessed using a pairwise Wilcoxon test with Holm p-value adjustment for multiple comparisons (*, p < 0.05; **, p < 0.01; ***, p < 0.001). b) Rarefaction curves of the top 200 ASVs for all six samples and all four seasons. Figure S2. The most abundant taxa as assessed by 16S rRNA gene amplicon data. Figure S3. Phycosphere composition as assessed by 16S rRNA gene amplicon data as a function of host species and season. Figure S4. Phylogenies and abundances of the 86 most abundant families as assessed by 16S rRNA gene amplicon sequencing. Figure S5. 16S rRNA phylogenetic tree reconstruction for 202 genera that were represented by at least three cultured strains. Figure S6. Compositional differences of strains depending on sample source and season. Figure S7. Numbers of colony forming units (CFUs) per gram of sample depending on habitat and season. Figure S8. Workflow for translating GTDB taxonomic classifications to SILVA taxonomic classifications. Figure S9. Proportions of genes within 965 metagenome-assembled genomes (MAGs) and 1,618 draft genomes (DGs) with EggNOG, COG (2020), Pfam, UniProtKB, and KEGG annotations, as well as the percentage of genes lacking any functional annotation. Figure S10. CAZymes in metagenome-assembled genomes (MAGs) and draft genomes (DGs) of different phyla. Figure S11. CAZymes versus sulfatase gene frequencies in prominent phyla and families as assessed in 1,294 metagenome-assembled genomes (MAGs) and 963 draft genomes (DGs) from all six sample sources. Figure S12. Categories of loci used to find putative PULs in this study. Figure S13. Histograms of the lengths of the four loci described in Fig. S12 in metagenome-assembled genomes (MAGs) and draft genomes (DGs). Figure S14. Tree of all 159 clusters derived from 3,769 PUL-associated SusC-like protein sequences from Bacteroidota metagenome-assembled genomes (MAGs) and draft genomes (DGs). Figure S15. Basic quality metrics of the 1,619 metagenome-assembled genomes (MAGs) and 965 draft genomes (DGs). Box-plots (A-E) show the minimum value, first quartile, median, third quartile and maximum value. Figure S16. Biosynthetic gene cluster (BGC) sizes in genomes from distinct phyla. Figure S17. Clustering of biosynthetic gene clusters (BGCs) according to sample type and phylogeny. Figure S18. Sizes of PULs and PUL-like loci in genomes from distinct Bacteroidota families (categories: hybrid susCD, single susCD, tandem repeat susCD, and tandem repeat plus hybrid susCD PULs).

Published
2023
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22. From Genomics to Microevolution and Ecology: The Case of Salinibacter ruber

Author

Peña, Arantxa, Teeling, Hanno, Huerta-Cepas, Jaime, Santos, Fernando, Meseguer, Inmaculada, Lucio, Marianna, Schmitt-Kopplin, Philippe, Dopazo, Joaquín, Rosselló-Móra, Ramon, Schüler, Margarete, Glöckner, Frank Oliver, Amann, Rudolf, Gabaldón, Toni, Antón, Josefa, Ventosa, Antonio, editor, Oren, Aharon, editor, and Ma, Yanhe, editor

Published
2011
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24. Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use

Author

Kleiner, Manuel, Wentrup, Cecilia, Lott, Christian, Teeling, Hanno, Wetzel, Silke, Young, Jacque, Chang, Yun-Juan, Shah, Manesh, VerBerkmoes, Nathan C., Zarzycki, Jan, Fuchs, Georg, Markert, Stephanie, Hempel, Kristina, Voigt, Birgit, Becher, Dörte, Liebeke, Manuel, Lalk, Michael, Albrecht, Dirk, Hecker, Michael, Schweder, Thomas, and Dubilier, Nicole

Published
2012

25. Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom

Author

Teeling, Hanno, Fuchs, Bernhard M., Becher, Dörte, Klockow, Christine, Gardebrecht, Antje, Bennke, Christin M., Kassabgy, Mariette, Huang, Sixing, Mann, Alexander ]., Waldmann, Jost, Weber, Marc, Klindworth, Anna, Otto, Andreas, Lange, Jana, Bernhardt, Jörg, Reinsch, Christine, Hecker, Michael, Peplies, Jörg, Bockelmann, Frank D., Callies, Ulrich, Gerdts, Gunnar, Wichels, Antje, Wiltshire, Karen H., Glöckner, Frank Oliver, Schweder, Thomas, and Amann, Rudolf

Published
2012
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27. Grazers affect the composition of dissolved storage glycans and thereby bacterioplankton composition during a biphasic North Sea spring algae bloom

Author

Sidhu, Chandni, primary, Kirstein, Inga V., additional, Meunier, Cédric L., additional, Rick, Johannes, additional, Wiltshire, Karen H., additional, Steinke, Nicola, additional, Vidal-Melgosa, Silvia, additional, Hehemann, Jan-Hendrik, additional, Huettel, Bruno, additional, Schweder, Thomas, additional, Fuchs, Bernhard M., additional, Amann, Rudolf I., additional, and Teeling, Hanno, additional

Published
2022
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31. Epiphytic common core bacteria in the microbiomes of co-located green (Ulva), brown (Saccharina) and red (Grateloupia, Gelidium) macroalgae.

Author

Lu, De-Chen, Wang, Feng-Qing, Amann, Rudolf I., Teeling, Hanno, and Du, Zong-Jun

Subjects
MARINE algae, ULVA, SACCHARINA, RED algae, BROWN algae, GREEN algae, CERAMIALES, LAMINARIA
Abstract

Background: Macroalgal epiphytic microbial communities constitute a rich resource for novel enzymes and compounds, but studies so far largely focused on tag-based microbial diversity analyses or limited metagenome sequencing of single macroalgal species. Results: We sampled epiphytic bacteria from specimens of Ulva sp. (green algae), Saccharina sp. (brown algae), Grateloupia sp. and Gelidium sp. (both red algae) together with seawater and sediment controls from a coastal reef in Weihai, China, during all seasons. Using 16S rRNA amplicon sequencing, we identified 14 core genera (consistently present on all macroalgae), and 14 dominant genera (consistently present on three of the macroalgae). Core genera represented ~ 0.7% of all genera, yet accounted for on average 51.1% of the bacterial abundances. Plate cultivation from all samples yielded 5,527 strains (macroalgae: 4,426) representing 1,235 species (685 potentially novel). Sequencing of selected strains yielded 820 non-redundant draft genomes (506 potentially novel), and sequencing of 23 sampled metagenomes yielded 1,619 metagenome-assembled genomes (MAGs), representing further 1,183 non-redundant genomes. 230 isolates and 153 genomes were obtained from the 28 core/dominant genera. We analyzed the genomic potential of phycosphere bacteria to degrade algal polysaccharides and to produce bioactive secondary metabolites. We predicted 4,451 polysaccharide utilization loci (PULs) and 8,810 biosynthetic gene clusters (BGCs). These were particularly prevalent in core/dominant genera. Conclusions: Our metabolic annotations and analyses of MAGs and genomes provide new insights into novel species of phycosphere bacteria and their ecological niches for an improved understanding of the macroalgal phycosphere microbiome. DnRc39z963CYrL7RdN5UNd Video Abstract [ABSTRACT FROM AUTHOR]

Published
2023
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35. Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader

Author

Werner, Johannes, Ferrer, Manuel, Michel, Gurvan, Mann, Alexander J., Huang, Sixing, Juarez, Silvia, Ciordia, Sergio, Albar, Juan P., Alcaide, María, La Cono, Violetta, Yakimov, Michail M., Antunes, André, Taborda, Marco, da Costa, Milton S., Hai, Tran, Glöckner, Frank Oliver, Golyshina, Olga V., Golyshin, Peter N., and Teeling, Hanno

Published
2014
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37. A genomic catalog of Earth’s microbiomes

Author

Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I. Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric, Allen, Michelle A., Alteio, Lauren V., Andersen, Gary, Anesio, Alexandre M., Attwood, Graeme, Avila-Magaña, Viridiana, Badis, Yacine, Bailey, Jake, Baker, Brett, Baldrian, Petr, Barton, Hazel A., Beck, David A.C., Becraft, Eric D., Beller, Harry R., Beman, J. Michael, Bernier-Latmani, Rizlan, Berry, Timothy D., Bertagnolli, Anthony, Bertilsson, Stefan, Bhatnagar, Jennifer M., Bird, Jordan T., Blanchard, Jeffrey L., Blumer-Schuette, Sara E., Bohannan, Brendan, Borton, Mikayla A., Brady, Allyson, Brawley, Susan H., Brodie, Juliet, Brown, Steven, Brum, Jennifer R., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Buckley, Daniel H., Buongiorno, Joy, Cadillo-Quiroz, Hinsby, Caffrey, Sean M., Campbell, Ashley N., Campbell, Barbara, Carr, Stephanie, Carroll, Jo Lynn, Cary, S. Craig, Cates, Anna M., Cattolico, Rose Ann, Cavicchioli, Ricardo, Chistoserdova, Ludmila, Coleman, Maureen L., Constant, Philippe, Conway, Jonathan M., Mac Cormack, Walter P., Crowe, Sean, Crump, Byron, Currie, Cameron, Daly, Rebecca, DeAngelis, Kristen M., Denef, Vincent, Denman, Stuart E., Desta, Adey, Dionisi, Hebe, Dodsworth, Jeremy, Dombrowski, Nina, Donohue, Timothy, Dopson, Mark, Driscoll, Timothy, Dunfield, Peter, Dupont, Christopher L., Dynarski, Katherine A., Edgcomb, Virginia, Edwards, Elizabeth A., Elshahed, Mostafa S., Figueroa, Israel, Flood, Beverly, Fortney, Nathaniel, Fortunato, Caroline S., Francis, Christopher, Gachon, Claire M.M., Garcia, Sarahi L., Gazitua, Maria C., Gentry, Terry, Gerwick, Lena, Gharechahi, Javad, Girguis, Peter, Gladden, John, Gradoville, Mary, Grasby, Stephen E., Gravuer, Kelly, Grettenberger, Christen L., Gruninger, Robert J., Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hausmann, Bela, Hazen, Terry C., Hedlund, Brian, Henny, Cynthia, Herfort, Lydie, Hernandez, Maria, Hershey, Olivia S., Hess, Matthias, Hollister, Emily B., Hug, Laura A., Hunt, Dana, Jansson, Janet, Jarett, Jessica, Kadnikov, Vitaly V., Kelly, Charlene, Kelly, Robert, Kelly, William, Kerfeld, Cheryl A., Kimbrel, Jeff, Klassen, Jonathan L., Konstantinidis, Konstantinos T., Lee, Laura L., Li, Wen Jun, Loder, Andrew J., Loy, Alexander, Lozada, Mariana, MacGregor, Barbara, Magnabosco, Cara, Maria da Silva, Aline, McKay, R. Michael, McMahon, Katherine, McSweeney, Chris S., Medina, Mónica, Meredith, Laura, Mizzi, Jessica, Mock, Thomas, Momper, Lily, Moran, Mary Ann, Morgan-Lang, Connor, Moser, Duane, Muyzer, Gerard, Myrold, David, Nash, Maisie, Nesbø, Camilla L., Neumann, Anthony P., Neumann, Rebecca B., Noguera, Daniel, Northen, Trent, Norton, Jeanette, Nowinski, Brent, Nüsslein, Klaus, O’Malley, Michelle A., Oliveira, Rafael S., Maia de Oliveira, Valeria, Onstott, Tullis, Osvatic, Jay, Ouyang, Yang, Pachiadaki, Maria, Parnell, Jacob, Partida-Martinez, Laila P., Peay, Kabir G., Pelletier, Dale, Peng, Xuefeng, Pester, Michael, Pett-Ridge, Jennifer, Peura, Sari, Pjevac, Petra, Plominsky, Alvaro M., Poehlein, Anja, Pope, Phillip B., Ravin, Nikolai, Redmond, Molly C., Reiss, Rebecca, Rich, Virginia, Rinke, Christian, Rodrigues, Jorge L.Mazza, Rodriguez-Reillo, William, Rossmassler, Karen, Sackett, Joshua, Salekdeh, Ghasem Hosseini, Saleska, Scott, Scarborough, Matthew, Schachtman, Daniel, Schadt, Christopher W., Schrenk, Matthew, Sczyrba, Alexander, Sengupta, Aditi, Setubal, Joao C., Shade, Ashley, Sharp, Christine, Sherman, David H., Shubenkova, Olga V., Sierra-Garcia, Isabel Natalia, Simister, Rachel, Simon, Holly, Sjöling, Sara, Slonczewski, Joan, Correa de Souza, Rafael Soares, Spear, John R., Stegen, James C., Stepanauskas, Ramunas, Stewart, Frank, Suen, Garret, Sullivan, Matthew, Sumner, Dawn, Swan, Brandon K., Swingley, Wesley, Tarn, Jonathan, Taylor, Gordon T., Teeling, Hanno, Tekere, Memory, Teske, Andreas, Thomas, Torsten, Thrash, Cameron, Tiedje, James, Ting, Claire S., Tully, Benjamin, Ulloa, Osvlado, Valentine, David L., Van Goethem, Marc W., VanderGheynst, Jean, Verbeke, Tobin J., Vollmers, John, Vuillemin, Aurèle, Waldo, Nicholas B., Williams, Timothy J., Tyson, Gene, Woodcroft, Ben, IMG/M Data Consortium, Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I. Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric, Allen, Michelle A., Alteio, Lauren V., Andersen, Gary, Anesio, Alexandre M., Attwood, Graeme, Avila-Magaña, Viridiana, Badis, Yacine, Bailey, Jake, Baker, Brett, Baldrian, Petr, Barton, Hazel A., Beck, David A.C., Becraft, Eric D., Beller, Harry R., Beman, J. Michael, Bernier-Latmani, Rizlan, Berry, Timothy D., Bertagnolli, Anthony, Bertilsson, Stefan, Bhatnagar, Jennifer M., Bird, Jordan T., Blanchard, Jeffrey L., Blumer-Schuette, Sara E., Bohannan, Brendan, Borton, Mikayla A., Brady, Allyson, Brawley, Susan H., Brodie, Juliet, Brown, Steven, Brum, Jennifer R., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Buckley, Daniel H., Buongiorno, Joy, Cadillo-Quiroz, Hinsby, Caffrey, Sean M., Campbell, Ashley N., Campbell, Barbara, Carr, Stephanie, Carroll, Jo Lynn, Cary, S. Craig, Cates, Anna M., Cattolico, Rose Ann, Cavicchioli, Ricardo, Chistoserdova, Ludmila, Coleman, Maureen L., Constant, Philippe, Conway, Jonathan M., Mac Cormack, Walter P., Crowe, Sean, Crump, Byron, Currie, Cameron, Daly, Rebecca, DeAngelis, Kristen M., Denef, Vincent, Denman, Stuart E., Desta, Adey, Dionisi, Hebe, Dodsworth, Jeremy, Dombrowski, Nina, Donohue, Timothy, Dopson, Mark, Driscoll, Timothy, Dunfield, Peter, Dupont, Christopher L., Dynarski, Katherine A., Edgcomb, Virginia, Edwards, Elizabeth A., Elshahed, Mostafa S., Figueroa, Israel, Flood, Beverly, Fortney, Nathaniel, Fortunato, Caroline S., Francis, Christopher, Gachon, Claire M.M., Garcia, Sarahi L., Gazitua, Maria C., Gentry, Terry, Gerwick, Lena, Gharechahi, Javad, Girguis, Peter, Gladden, John, Gradoville, Mary, Grasby, Stephen E., Gravuer, Kelly, Grettenberger, Christen L., Gruninger, Robert J., Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hausmann, Bela, Hazen, Terry C., Hedlund, Brian, Henny, Cynthia, Herfort, Lydie, Hernandez, Maria, Hershey, Olivia S., Hess, Matthias, Hollister, Emily B., Hug, Laura A., Hunt, Dana, Jansson, Janet, Jarett, Jessica, Kadnikov, Vitaly V., Kelly, Charlene, Kelly, Robert, Kelly, William, Kerfeld, Cheryl A., Kimbrel, Jeff, Klassen, Jonathan L., Konstantinidis, Konstantinos T., Lee, Laura L., Li, Wen Jun, Loder, Andrew J., Loy, Alexander, Lozada, Mariana, MacGregor, Barbara, Magnabosco, Cara, Maria da Silva, Aline, McKay, R. Michael, McMahon, Katherine, McSweeney, Chris S., Medina, Mónica, Meredith, Laura, Mizzi, Jessica, Mock, Thomas, Momper, Lily, Moran, Mary Ann, Morgan-Lang, Connor, Moser, Duane, Muyzer, Gerard, Myrold, David, Nash, Maisie, Nesbø, Camilla L., Neumann, Anthony P., Neumann, Rebecca B., Noguera, Daniel, Northen, Trent, Norton, Jeanette, Nowinski, Brent, Nüsslein, Klaus, O’Malley, Michelle A., Oliveira, Rafael S., Maia de Oliveira, Valeria, Onstott, Tullis, Osvatic, Jay, Ouyang, Yang, Pachiadaki, Maria, Parnell, Jacob, Partida-Martinez, Laila P., Peay, Kabir G., Pelletier, Dale, Peng, Xuefeng, Pester, Michael, Pett-Ridge, Jennifer, Peura, Sari, Pjevac, Petra, Plominsky, Alvaro M., Poehlein, Anja, Pope, Phillip B., Ravin, Nikolai, Redmond, Molly C., Reiss, Rebecca, Rich, Virginia, Rinke, Christian, Rodrigues, Jorge L.Mazza, Rodriguez-Reillo, William, Rossmassler, Karen, Sackett, Joshua, Salekdeh, Ghasem Hosseini, Saleska, Scott, Scarborough, Matthew, Schachtman, Daniel, Schadt, Christopher W., Schrenk, Matthew, Sczyrba, Alexander, Sengupta, Aditi, Setubal, Joao C., Shade, Ashley, Sharp, Christine, Sherman, David H., Shubenkova, Olga V., Sierra-Garcia, Isabel Natalia, Simister, Rachel, Simon, Holly, Sjöling, Sara, Slonczewski, Joan, Correa de Souza, Rafael Soares, Spear, John R., Stegen, James C., Stepanauskas, Ramunas, Stewart, Frank, Suen, Garret, Sullivan, Matthew, Sumner, Dawn, Swan, Brandon K., Swingley, Wesley, Tarn, Jonathan, Taylor, Gordon T., Teeling, Hanno, Tekere, Memory, Teske, Andreas, Thomas, Torsten, Thrash, Cameron, Tiedje, James, Ting, Claire S., Tully, Benjamin, Ulloa, Osvlado, Valentine, David L., Van Goethem, Marc W., VanderGheynst, Jean, Verbeke, Tobin J., Vollmers, John, Vuillemin, Aurèle, Waldo, Nicholas B., Williams, Timothy J., Tyson, Gene, Woodcroft, Ben, and IMG/M Data Consortium

Abstract

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

Published
2021

47. Filogenómica de Bacteroidetes; radiación adaptativa del filo explicada por su cadena respiratoria

Author

Muñoz, Raúl, Teeling, Hanno, Amann, Rudolf, Rosselló-Mora, Ramón, Muñoz, Raúl, Teeling, Hanno, Amann, Rudolf, and Rosselló-Mora, Ramón

Abstract

Cultivable mayoritarios: Firmicutes, Actinobacteria, Proteobacteria y Bacteroidetes, el último es el más difícil de categorizar fenotípicamente. La filogenia del ARN desveló su monofilia a finales de los 80, y las técnicas de secuenciación masiva su abundancia en muchos ambientes, que había sido subestimada por técnicas de cultivo y librerías de clones. Aprovechando el reciente crecimiento de las bases de datos de genomas, hemos seleccionado 89 genomas representativos de la diversidad de este filo para compararlos por ¿Pairwise Reciprocal Best Match¿, sintenia y mediana de identidades ortólogas (m.s.i.). Las tendencias que observamos en conservación de secuencias en este filo nos han permitido explicar, por ejemplo, el origen aerobio de Bacteroidales y aportar pruebas para su definición como nanaerobios en lugar de anaerobios. Hemos podido constatar la presencia del sistema de secreción IX (T9SS) en el 90% de los genomas. Y describir la presencia del súper-complejo respiratorio ACIII-caa3COX en el 83%; todos los organismos aerobios. Por último, hemos encontrado que los Bacteroidetes halófilos se adaptan al ambiente salino por la sustitución del complejo I respiratorio por un complejo Na+-NQR mediante transferencia horizontal. Con todo ello hemos podido explicar la historia evolutiva del filo por radiación adaptativa.

Published
2020

48. Ancestry and adaptive radiation of Bacteroidetes as assessed by comparative genomics

Author

Max Planck Society, Ministerio de Ciencia, Innovación y Universidades (España), Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), European Commission, Deep Blue Sea Enterprise, Max Planck Institute for Marine Microbiology, Ministerio de Educación, Cultura y Deporte (España), Muñoz, Raúl, Teeling, Hanno, Amann, Rudolf, Rosselló-Mora, Ramón, Max Planck Society, Ministerio de Ciencia, Innovación y Universidades (España), Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), European Commission, Deep Blue Sea Enterprise, Max Planck Institute for Marine Microbiology, Ministerio de Educación, Cultura y Deporte (España), Muñoz, Raúl, Teeling, Hanno, Amann, Rudolf, and Rosselló-Mora, Ramón

Abstract

To date, the phylum Bacteroidetes comprises more than 1,500 described species with diverse ecological roles. However, there is little understanding of archetypal Bacteroidetes traits at a genomic level. In this study, a representative set of 89 Bacteroidetes genomes was compiled, and pairwise reciprocal best-match gene comparisons and gene syntenies were used to identify common traits that allowed Bacteroidetes evolution and adaptive radiation to be traced. The type IX secretion system (T9SS) was highly conserved among all studied Bacteroidetes. Class-level comparisons furthermore suggested that the ACIII-caa3COX super-complex evolved in the ancestral aerobic bacteroidetal lineage, and was secondarily lost in extant anaerobic Bacteroidetes. Another Bacteroidetes-specific respiratory chain adaptation was the sodium-pumping Nqr complex I that replaced the ancestral proton-pumping complex I in marine species. T9SS plays a role in gliding motility and the acquisition of complex macro-molecular organic compounds, and the ACIII-caa3COX super-complex allows effective control of electron flux during respiration. This combination likely provided ancestral Bacteroidetes with a decisive competitive advantage to effectively scavenge, uptake and degrade complex organic molecules, and therefore has played a pivotal role in the successful adaptive radiation of the phylum.

Published
2020

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