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1. The nature of the last universal common ancestor and its impact on the early Earth system

Author

Moody, Edmund R. R., Álvarez-Carretero, Sandra, Mahendrarajah, Tara A., Clark, James W., Betts, Holly C., Dombrowski, Nina, Szánthó, Lénárd L., Boyle, Richard A., Daines, Stuart, Chen, Xi, Lane, Nick, Yang, Ziheng, Shields, Graham A., Szöllősi, Gergely J., Spang, Anja, Pisani, Davide, Williams, Tom A., Lenton, Timothy M., and Donoghue, Philip C. J.

Published
2024
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2. The parasitic lifestyle of an archaeal symbiont

Author

Hamm, Joshua N., Liao, Yan, von Kügelgen, Andriko, Dombrowski, Nina, Landers, Evan, Brownlee, Christopher, Johansson, Emma M. V., Whan, Renee M., Baker, Matthew A. B., Baum, Buzz, Bharat, Tanmay A. M., Duggin, Iain G., Spang, Anja, and Cavicchioli, Ricardo

Published
2024
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3. Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

Author

Eme, Laura, Tamarit, Daniel, Caceres, Eva F, Stairs, Courtney W, De Anda, Valerie, Schön, Max E, Seitz, Kiley W, Dombrowski, Nina, Lewis, William H, Homa, Felix, Saw, Jimmy H, Lombard, Jonathan, Nunoura, Takuro, Li, Wen-Jun, Hua, Zheng-Shuang, Chen, Lin-Xing, Banfield, Jillian F, John, Emily St, Reysenbach, Anna-Louise, Stott, Matthew B, Schramm, Andreas, Kjeldsen, Kasper U, Teske, Andreas P, Baker, Brett J, and Ettema, Thijs JG

Subjects
Genetics, Biotechnology, Generic health relevance, Archaea, Eukaryota, Eukaryotic Cells, Phylogeny, Prokaryotic Cells, Datasets as Topic, Gene Duplication, Evolution, Molecular, General Science & Technology
Abstract

In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2-4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.

Published
2023

4. Chapter 21 Archaea

Author

Dombrowski, Nina, Mahendrarajah, Tara, Gross, Sarah T., Eme, Laura, and Spang, Anja

Subjects
Antisepsis, Bacteria, Bacteriophage, Business of Microbiology, Disinfection, Fungi, Microbiology, Microbiology procedures, parasites, sterilization, virus, thema EDItEUR::P Mathematics and Science::PD Science: general issues, thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical), thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSD Molecular biology, thema EDItEUR::P Mathematics and Science::PS Biology, life sciences, thema EDItEUR::R Earth Sciences, Geography, Environment, Planning::RN The environment::RNC Applied ecology::RNCB Biodiversity
Abstract

Practical Handbook of Microbiology, 4th edition provides basic, clear and concise knowledge and practical information about working with microorganisms. Useful to anyone interested in microbes, the book is intended to especially benefit four groups: trained microbiologists working within one specific area of microbiology; people with training in other disciplines, and use microorganisms as a tool or "chemical reagent"; business people evaluating investments in microbiology focused companies; and an emerging group, people in occupations and trades that might have limited training in microbiology, but who require specific practical information.

Published
2021
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7. Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways.

Author

De Anda, Valerie, Chen, Lin-Xing, Dombrowski, Nina, Hua, Zheng-Shuang, Jiang, Hong-Chen, Banfield, Jillian F, Li, Wen-Jun, and Baker, Brett J

Subjects
Archaea, Carbon, Methane, RNA, Ribosomal, 16S, Hot Springs, Phylogeny, Species Specificity, Genome, Archaeal, Geography, Geologic Sediments, China, Metagenome, Carbon Cycle, Hydrothermal Vents, RNA, Ribosomal, 16S, Genome, Archaeal
Abstract

Geothermal environments, such as hot springs and hydrothermal vents, are hotspots for carbon cycling and contain many poorly described microbial taxa. Here, we reconstructed 15 archaeal metagenome-assembled genomes (MAGs) from terrestrial hot spring sediments in China and deep-sea hydrothermal vent sediments in Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct group within the TACK superphylum, and thus we propose their classification as a new phylum, 'Brockarchaeota', named after Thomas Brock for his seminal research in hot springs. Based on the MAG sequence information, we infer that some Brockarchaeota are uniquely capable of mediating non-methanogenic anaerobic methylotrophy, via the tetrahydrofolate methyl branch of the Wood-Ljungdahl pathway and reductive glycine pathway. The hydrothermal vent genotypes appear to be obligate fermenters of plant-derived polysaccharides that rely mostly on substrate-level phosphorylation, as they seem to lack most respiratory complexes. In contrast, hot spring lineages have alternate pathways to increase their ATP yield, including anaerobic methylotrophy of methanol and trimethylamine, and potentially use geothermally derived mercury, arsenic, or hydrogen. Their broad distribution and their apparent anaerobic metabolic versatility indicate that Brockarchaeota may occupy previously overlooked roles in anaerobic carbon cycling.

Published
2021

9. An archaeal symbiont-host association from the deep terrestrial subsurface

Author

Schwank, Katrin, Bornemann, Till LV, Dombrowski, Nina, Spang, Anja, Banfield, Jillian F, and Probst, Alexander J

Subjects
Microbiology, Biological Sciences, Archaea, Ecosystem, Genome, Archaeal, Groundwater, In Situ Hybridization, Fluorescence, Metagenome, Nanoarchaeota, Phylogeny, Symbiosis, Utah, Environmental Sciences, Technology, Biological sciences, Environmental sciences
Abstract

DPANN archaea have reduced metabolic capacities and are diverse and abundant in deep aquifer ecosystems, yet little is known about their interactions with other microorganisms that reside there. Here, we provide evidence for an archaeal host-symbiont association from a deep aquifer system at the Colorado Plateau (Utah, USA). The symbiont, Candidatus Huberiarchaeum crystalense, and its host, Ca. Altiarchaeum hamiconexum, show a highly significant co-occurrence pattern over 65 metagenome samples collected over six years. The physical association of the two organisms was confirmed with genome-informed fluorescence in situ hybridization depicting small cocci of Ca. H. crystalense attached to Ca. A. hamiconexum cells. Based on genomic information, Ca. H. crystalense potentially scavenges vitamins, sugars, nucleotides, and reduced redox-equivalents from its host and thus has a similar metabolism as Nanoarchaeum equitans. These results provide insight into host-symbiont interactions among members of two uncultivated archaeal phyla that thrive in a deep subsurface aquifer.

Published
2019

13. Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota

Author

Chen, Lin-Xing, Méndez-García, Celia, Dombrowski, Nina, Servín-Garcidueñas, Luis E, Eloe-Fadrosh, Emiley A, Fang, Bao-Zhu, Luo, Zhen-Hao, Tan, Sha, Zhi, Xiao-Yang, Hua, Zheng-Shuang, Martinez-Romero, Esperanza, Woyke, Tanja, Huang, Li-Nan, Sánchez, Jesús, Peláez, Ana Isabel, Ferrer, Manuel, Baker, Brett J, and Shu, Wen-Sheng

Subjects
Microbiology, Biological Sciences, Genetics, Amino Acids, Archaea, Biodiversity, Biological Evolution, Carbon, Fresh Water, Genome, Archaeal, Genomics, Hot Springs, Iron, Nitrogen, Nitrogen Cycle, Phylogeny, RNA, Ribosomal, 16S, Environmental Sciences, Technology, Biological sciences, Environmental sciences
Abstract

Small acidophilic archaea belonging to Micrarchaeota and Parvarchaeota phyla are known to physically interact with some Thermoplasmatales members in nature. However, due to a lack of cultivation and limited genomes on hand, their biodiversity, metabolisms, and physiologies remain largely unresolved. Here, we obtained 39 genomes from acid mine drainage (AMD) and hot spring environments around the world. 16S rRNA gene based analyses revealed that Parvarchaeota were only detected in AMD and hot spring habitats, while Micrarchaeota were also detected in others including soil, peat, hypersaline mat, and freshwater, suggesting a considerable higher diversity and broader than expected habitat distribution for this phylum. Despite their small genomes (0.64-1.08 Mb), these archaea may contribute to carbon and nitrogen cycling by degrading multiple saccharides and proteins, and produce ATP via aerobic respiration and fermentation. Additionally, we identified several syntenic genes with homology to those involved in iron oxidation in six Parvarchaeota genomes, suggesting their potential role in iron cycling. However, both phyla lack biosynthetic pathways for amino acids and nucleotides, suggesting that they likely scavenge these biomolecules from the environment and/or other community members. Moreover, low-oxygen enrichments in laboratory confirmed our speculation that both phyla are microaerobic/anaerobic, based on several specific genes identified in them. Furthermore, phylogenetic analyses provide insights into the close evolutionary history of energy related functionalities between both phyla with Thermoplasmatales. These results expand our understanding of these elusive archaea by revealing their involvement in carbon, nitrogen, and iron cycling, and suggest their potential interactions with Thermoplasmatales on genomic scale.

Published
2018

14. Archaea

Author

Dombrowski, Nina, primary, Mahendrarajah, Tara, additional, Gross, Sarah T., additional, Eme, Laura, additional, and Spang, Anja, additional

Published
2021
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20. Archaea – An Introduction

Author

Blohs, Marcus, primary, Mahnert, Alexander, additional, Spang, Anja, additional, Dombrowski, Nina, additional, Krupovic, Mart, additional, and Klingl, Andreas, additional

Published
2019
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21. ATP synthase evolution on a cross-braced dated tree of life

Author

Mahendrarajah, Tara A., primary, Moody, Edmund R. R., additional, Schrempf, Dominik, additional, Szánthó, Lénárd L., additional, Dombrowski, Nina, additional, Davín, Adrián A., additional, Pisani, Davide, additional, Donoghue, Philip C. J., additional, Szöllősi, Gergely J., additional, Williams, Tom A., additional, and Spang, Anja, additional

Published
2023
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22. Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

Author

Eme, Laura, primary, Tamarit, Daniel, additional, Caceres, Eva F., additional, Stairs, Courtney W., additional, Anda, Valerie De, additional, Schön, Max E., additional, Seitz, Kiley W., additional, Dombrowski, Nina, additional, Lewis, William H., additional, Homa, Felix, additional, Saw, Jimmy H., additional, Lombard, Jonathan, additional, Nunoura, Takuro, additional, Li, Wen-Jun, additional, Hua, Zheng-Shuang, additional, Chen, Lin-Xing, additional, Banfield, Jillian F., additional, John, Emily St, additional, Reysenbach, Anna-Louise, additional, Stott, Matthew B., additional, Schramm, Andreas, additional, Kjeldsen, Kasper U., additional, Teske, Andreas P., additional, Baker, Brett J., additional, and Ettema, Thijs J. G., additional

Published
2023
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23. Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

Author

Sub Bioinformatics, Theoretical Biology and Bioinformatics, Eme, Laura, Tamarit, Daniel, Caceres, Eva F., Stairs, Courtney W., Anda, Valerie De, Schön, Max E., Seitz, Kiley W., Dombrowski, Nina, Lewis, William H., Homa, Felix, Saw, Jimmy H., Lombard, Jonathan, Nunoura, Takuro, Li, Wen-Jun, Hua, Zheng-Shuang, Chen, Lin-Xing, Banfield, Jillian F., John, Emily St, Reysenbach, Anna-Louise, Stott, Matthew B., Schramm, Andreas, Kjeldsen, Kasper U., Teske, Andreas P., Baker, Brett J., Ettema, Thijs J. G., Sub Bioinformatics, Theoretical Biology and Bioinformatics, Eme, Laura, Tamarit, Daniel, Caceres, Eva F., Stairs, Courtney W., Anda, Valerie De, Schön, Max E., Seitz, Kiley W., Dombrowski, Nina, Lewis, William H., Homa, Felix, Saw, Jimmy H., Lombard, Jonathan, Nunoura, Takuro, Li, Wen-Jun, Hua, Zheng-Shuang, Chen, Lin-Xing, Banfield, Jillian F., John, Emily St, Reysenbach, Anna-Louise, Stott, Matthew B., Schramm, Andreas, Kjeldsen, Kasper U., Teske, Andreas P., Baker, Brett J., and Ettema, Thijs J. G.

Published
2023

25. The intracellular lifestyle of an archaeal symbiont

Author

Hamm, Joshua Norman, primary, Liao, Yan, additional, von Kügelgen, Andriko, additional, Dombrowski, Nina, additional, Landers, Evan, additional, Brownlee, Christopher, additional, Johansson, Emma M. V., additional, Whan, Renee M., additional, Baker, Matthew A. B., additional, Baum, Buzz, additional, Bharat, Tanmay A. M., additional, Duggin, Iain G., additional, Spang, Anja, additional, and Cavicchioli, Ricardo, additional

Published
2023
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30. Functional overlap of the Arabidopsis leaf and root microbiota

Author

Bai, Yang, Muller, Daniel B., Srinivas, Girish, Garrido-Oter, Ruben, Potthoff, Eva, Rott, Matthias, Dombrowski, Nina, Munch, Philipp C., Spaepen, Stijn, Remus-Emsermann, Mitja, Huttel, Bruno, McHardy, Alice C., Vorholt, Julia A., and Schulze-Lefert, Paul

Subjects
Plants -- Research, Microbiota (Symbiotic organisms) -- Research, Arabidopsis thaliana -- Research -- Development and progression -- Care and treatment -- Complications and side effects -- Patient outcomes, Genomes -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Roots and leaves of healthy plants host taxonomically structured bacterial assemblies, and members of these communities contribute to plant growth and health. We established Arabidopsis leaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community sequencing. We found an extensive taxonomic overlap between the leaf and root microbiota. Genome drafts of 400 isolates revealed a large overlap of genome-encoded functional capabilities between leaf- and root-derived bacteria with few significant differences at the level of individual functional categories. Using defined bacterial communities and a gnotobiotic Arabidopsis plant system we show that the isolates form assemblies resembling natural microbiota on their cognate host organs, but are also capable of ectopic leaf or root colonization. While this raises the possibility of reciprocal relocation between root and leaf microbiota members, genome information and recolonization experiments also provide evidence for microbiota specialization to their respective niche., Plants and animals harbour abundant and diverse bacterial microbiota (1). These taxonomically structured bacterial communities have important functions for the health of their multicellular eukaryotic hosts (2-4). The leaf and [...]

Published
2015
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32. An estimate of the deepest branches of the tree of life from ancient vertically evolving genes

Author

Moody, Edmund R. R., Mahendrarajah, Tara A., Dombrowski, Nina, Clark, James W., Petitjean, Celine, Offre, Pierre, Szollosi, Gergely J., Spang, Anja, Williams, Tom A., Perry, George H., Moody, Edmund R. R., Mahendrarajah, Tara A., Dombrowski, Nina, Clark, James W., Petitjean, Celine, Offre, Pierre, Szollosi, Gergely J., Spang, Anja, Williams, Tom A., and Perry, George H.

Abstract

Core gene phylogenies provide a window into early evolution, but different gene sets and analytical methods have yielded substantially different views of the tree of life. Trees inferred from a small set of universal core genes have typically supported a long branch separating the archaeal and bacterial domains. By contrast, recent analyses of a broader set of non-ribosomal genes have suggested that Archaea may be less divergent from Bacteria, and that estimates of inter-domain distance are inflated due to accelerated evolution of ribosomal proteins along the inter-domain branch. Resolving this debate is key to determining the diversity of the archaeal and bacterial domains, the shape of the tree of life, and our understanding of the early course of cellular evolution. Here, we investigate the evolutionary history of the marker genes key to the debate. We show that estimates of a reduced Archaea-Bacteria (AB) branch length result from inter-domain gene transfers and hidden paralogy in the expanded marker gene set. By contrast, analysis of a broad range of manually curated marker gene datasets from an evenly sampled set of 700 Archaea and Bacteria reveals that current methods likely underestimate the AB branch length due to substitutional saturation and poor model fit; that the best-performing phylogenetic markers tend to support longer inter-domain branch lengths; and that the AB branch lengths of ribosomal and non-ribosomal marker genes are statistically indistinguishable. Furthermore, our phylogeny inferred from the 27 highest-ranked marker genes recovers a clade of DPANN at the base of the Archaea and places the bacterial Candidate Phyla Radiation (CPR) within Bacteria as the sister group to the Chloroflexota.

Published
2022
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37. Archaea

Author

Dombrowski, Nina, Mahendrarajah, Tara, Gross, Sarah, Eme, Laura, Spang, Anja, Ecologie Systématique et Evolution (ESE), and AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021

39. A diverse uncultivated microbial community is responsible for organic matter degradation in the Black Sea sulphidic zone

Author

Suominen, Saara, Dombrowski, Nina, Sinninghe Damsté, Jaap S., Villanueva, Laura, Suominen, Saara, Dombrowski, Nina, Sinninghe Damsté, Jaap S., and Villanueva, Laura

Abstract

Organic matter degradation in marine environments is essential for the recycling of nutrients, especially under conditions of anoxia where organic matter tends to accumulate. However, little is known about the diversity of the microbial communities responsible for the mineralization of organic matter in the absence of oxygen, as well as the factors controlling their activities. Here, we determined the active heterotrophic prokaryotic community in the sulphidic water column of the Black Sea, an ideal model system, where a tight coupling between carbon, nitrogen and sulphur cycles is expected. Active microorganisms degrading both dissolved organic matter (DOM) and protein extracts were determined using quantitative DNA stable isotope probing incubation experiments. These results were compared with the metabolic potential of metagenome-assembled genomes obtained from the water column. Organic matter incubations showed that groups like Cloacimonetes and Marinimicrobia are generalists degrading DOM. Based on metagenomic profiles the degradation proceeds in a potential interaction with members of the Deltaproteobacteria and Chloroflexi Dehalococcoidia. On the other hand, microbes with small genomes like the bacterial phyla Parcubacteria, Omnitrophica and of the archaeal phylum Woesearchaeota, were the most active, especially in protein-amended incubations, revealing the potential advantage of streamlined microorganisms in highly reduced conditions.

Published
2021

41. 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

42. Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities

Author

Reysenbach, Anna-Louise, St. John, Emily, Meneghin, Jennifer, Flores, Gilberto, Podar, Mircea, Dombrowski, Nina, Spang, Anja, L’Haridon, Stephane, Humphris, Susan E., de Ronde, Cornel E. J., Tontini, F. Caratori, Tivey, Maurice A., Stucker, Valerie, Stewart, Lucy C., Diehl, Alexander, Bach, Wolfgang, Reysenbach, Anna-Louise, St. John, Emily, Meneghin, Jennifer, Flores, Gilberto, Podar, Mircea, Dombrowski, Nina, Spang, Anja, L’Haridon, Stephane, Humphris, Susan E., de Ronde, Cornel E. J., Tontini, F. Caratori, Tivey, Maurice A., Stucker, Valerie, Stewart, Lucy C., Diehl, Alexander, and Bach, Wolfgang

Abstract

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Reysenbach, A. L., St John, E., Meneghin, J., Flores, G. E., Podar, M., Dombrowski, N., Spang, A., L'Haridon, S., Humphris, S. E., de Ronde, C. E. J., Caratori Tontini, F., Tivey, M., Stucker, V. K., Stewart, L. C., Diehl, A., & Bach, W. Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities. Proceedings of the National Academy of Sciences of the United States of America, 117(51), (2020): 202019021, doi:10.1073/pnas.2019021117., Hydrothermally active submarine volcanoes are mineral-rich biological oases contributing significantly to chemical fluxes in the deep sea, yet little is known about the microbial communities inhabiting these systems. Here we investigate the diversity of microbial life in hydrothermal deposits and their metagenomics-inferred physiology in light of the geological history and resulting hydrothermal fluid paths in the subsurface of Brothers submarine volcano north of New Zealand on the southern Kermadec arc. From metagenome-assembled genomes we identified over 90 putative bacterial and archaeal genomic families and nearly 300 previously unknown genera, many potentially endemic to this submarine volcanic environment. While magmatically influenced hydrothermal systems on the volcanic resurgent cones of Brothers volcano harbor communities of thermoacidophiles and diverse members of the superphylum “DPANN,” two distinct communities are associated with the caldera wall, likely shaped by two different types of hydrothermal circulation. The communities whose phylogenetic diversity primarily aligns with that of the cone sites and magmatically influenced hydrothermal systems elsewhere are characterized predominately by anaerobic metabolisms. These populations are probably maintained by fluids with greater magmatic inputs that have interacted with different (deeper) previously altered mineral assemblages. However, proximal (a few meters distant) communities with gene-inferred aerobic, microaerophilic, and anaerobic metabolisms are likely supported by shallower seawater-dominated circulation. Furthermore, mixing of fluids from these two distinct hydrothermal circulation systems may have an underlying imprint on the high microbial phylogenomic diversity. Collectively our results highlight the importance of considering geologic evolution and history of subsurface processes in studying microbial colonization and community dynamics in volcanic environments., We thank the captain and crew of the R/V Thompson and the engineers from Woods Hole Oceanographic Institution for the successful operation of ROV Jason. The project was funded by NSF grants OCE‐1558356 (Principal Investigator S.E.H.) and OCE-1558795 (Principal Investigator A.-L.R.). S.L. received a grant from the University of Brest to work in the A.-L.R. laboratory. A travel fund from Interridge enabled A.D. to participate on the R/V Thompson cruise. Funding for this work for C.E.J.d.R., F.C.T., V.K.S., and L.C.S. was provided by the New Zealand government. A.S. was supported by the Swedish Research Council (Vetenskapsrådet starting grant 2016-03559 to A.S.) and the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Dutch Research Council) Foundation of the Netherlands Organization for Scientific Research (Women In Science Excel [WISE] fellowship to A.S.). A.-L.R. and E.S.J. thank Rika Anderson for helpful methodological discussions and Sean Sylva for assistance in shipboard geochemical analysis.

Published
2021

44. Unraveling the critical growth factors for stable cultivation of (nano-sized) Micrarchaeota

Author

Krause, Susanne, primary, Gfrerer, Sabrina, additional, Reuse, Carsten, additional, Dombrowski, Nina, additional, Villanueva, Laura, additional, Bunk, Boyke, additional, Spröer, Cathrin, additional, Neu, Thomas R., additional, Kuhlicke, Ute, additional, Schmidt-Hohagen, Kerstin, additional, Hiller, Karsten, additional, Rachel, Reinhard, additional, Spang, Anja, additional, and Gescher, Johannes, additional

Published
2021
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