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Moore CJ, Bornemann TLV, Figueroa-Gonzalez PA, Esser SP, Moraru C, Soares AR, Hinzke T, Trautwein-Schult A, Maaß S, Becher D, Starke J, Plewka J, Rothe L, Probst AJ. Time-series metaproteogenomics of a high-CO 2 aquifer reveals active viruses with fluctuating abundances and broad host ranges. MICROLIFE 2024; 5:uqae011. [PMID: 38855384 PMCID: PMC11162154 DOI: 10.1093/femsml/uqae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/05/2024] [Accepted: 05/18/2024] [Indexed: 06/11/2024]
Abstract
Ecosystems subject to mantle degassing are of particular interest for understanding global biogeochemistry, as their microbiomes are shaped by prolonged exposure to high CO2 and have recently been suggested to be highly active. While the genetic diversity of bacteria and archaea in these deep biosphere systems have been studied extensively, little is known about how viruses impact these microbial communities. Here, we show that the viral community in a high-CO2 cold-water geyser (Wallender Born, Germany) undergoes substantial fluctuations over a period of 12 days, although the corresponding prokaryotic community remains stable, indicating a newly observed "infect to keep in check" strategy that maintains prokaryotic community structure. We characterized the viral community using metagenomics and metaproteomics, revealing 8 654 viral operational taxonomic units (vOTUs). CRISPR spacer-to-protospacer matching linked 278 vOTUs to 32 hosts, with many vOTUs sharing hosts from different families. High levels of viral structural proteins present in the metaproteome (several structurally annotated based on AlphaFold models) indicate active virion production at the time of sampling. Viral genomes expressed many proteins involved in DNA metabolism and manipulation, and encoded for auxiliary metabolic genes, which likely bolster phosphate and sulfur metabolism of their hosts. The active viral community encodes genes to facilitate acquisition and transformation of host nutrients, and appears to consist of many nutrient-demanding members, based on abundant virion proteins. These findings indicate viruses are inextricably linked to the biogeochemical cycling in this high-CO2 environment and substantially contribute to prokaryotic community stability in the deep biosphere hotspots.
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Affiliation(s)
- Carrie Julia Moore
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University Duisburg-Essen, 45141 Essen, Germany
| | - Till L V Bornemann
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University Duisburg-Essen, 45141 Essen, Germany
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Perla Abigail Figueroa-Gonzalez
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University Duisburg-Essen, 45141 Essen, Germany
| | - Sarah P Esser
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University Duisburg-Essen, 45141 Essen, Germany
| | - Cristina Moraru
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University Duisburg-Essen, 45141 Essen, Germany
| | - André Rodrigues Soares
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University Duisburg-Essen, 45141 Essen, Germany
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Tjorven Hinzke
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
- Department of Pathogen Evolution, Helmholtz Institute for One Health, 17489 Greifswald, Germany
| | - Anke Trautwein-Schult
- Microbial Proteomics, Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
| | - Sandra Maaß
- Microbial Proteomics, Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
| | - Dörte Becher
- Microbial Proteomics, Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
| | - Joern Starke
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University Duisburg-Essen, 45141 Essen, Germany
| | - Julia Plewka
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University Duisburg-Essen, 45141 Essen, Germany
| | - Lousia Rothe
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Alexander J Probst
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University Duisburg-Essen, 45141 Essen, Germany
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
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Göker M, Oren A. Valid publication of names of two domains and seven kingdoms of prokaryotes. Int J Syst Evol Microbiol 2024; 74. [PMID: 38252124 DOI: 10.1099/ijsem.0.006242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024] Open
Abstract
The International Code of Nomenclature of Prokaryotes (ICNP) now includes the categories domain and kingdom. For the purpose of the valid publication of their names under the ICNP, we consider here the two known domains, 'Bacteria' and 'Archaea', as well as a number of taxa suitable for the rank of kingdom, based on previous phylogenetic and taxonomic studies. It is proposed to subdivide the domain Bacteria into the kingdoms Bacillati, Fusobacteriati, Pseudomonadati and Thermotogati. This arrangement reflects contemporary phylogenetic hypotheses as well as previous taxonomic proposals based on cell wall structure, including 'diderms' vs. 'monoderms', Gracilicutes vs. Firmicutes, 'Negibacteria' vs. 'Unibacteria', 'Hydrobacteria' vs. 'Terrabacteria', and 'Hydrobacterida' vs. 'Terrabacterida'. The domain Archaea is proposed to include the kingdoms Methanobacteriati, Nanobdellati and Thermoproteati, reflecting the previous division into 'Euryarchaeota', 'DPANN superphylum' and 'TACK superphylum'.
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Affiliation(s)
- Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Aharon Oren
- The Hebrew University of Jerusalem, The Institute of Life Sciences, Edmond J. Safra Campus - Givat Ram, 9190401 Jerusalem, Israel
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Reysenbach AL, Terns MP. CRISPR-influenced symbiosis. Nat Microbiol 2023; 8:1611-1612. [PMID: 37580593 PMCID: PMC10791070 DOI: 10.1038/s41564-023-01445-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
CRISPR systems canonically confer microorganisms with protection against invading viral DNA, plasmids and mobile genetic elements, however a multi-omics investigation of deep subsurface archaeal communities suggests that archaeal CRISPR systems might target other archaeal parasites or force a transition from parasitism to mutualism.
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Affiliation(s)
- Anna-Louise Reysenbach
- Center for Life in Extreme Environments, Biology Department, Portland State University, Portland, OR, USA.
| | - Michael P Terns
- Biochemistry and Molecular Biology, Genetics and Microbiology, University of Georgia, Athens, GA, USA.
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