ArticleMicrobiome2024
Metaproteogenomics resolution of a high-CO
Article in Microbiome, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Ammonia oxidation and recalcitrant carbon degradation fuel mixotrophic growth in the symbiont community of a deep-sea sponge.Microbiome · 2026Article
- Growth of candidate phyla radiation bacteria in groundwater incubations reveals widespread adaptations to oxic conditions.Microbiome · 2025Article
- Acquisition of Spacers from Foreign Prokaryotic Genomes by CRISPR-Cas Systems in Natural Environments.Genome biology and evolution · 2025Article
- Microbial diversity and functional potential of the Halobates melleus (Heteroptera: Gerridae) microbiome from the Red Sea coastline.Environmental microbiome · 2025Article
- Multi-Metagenome Analysis Unravels Community Collapse After Sampling and Hints the Cultivation Strategy of CPR Bacteria in Groundwater.Microorganisms · 2025Article
- Time-series metaproteogenomics of a high-COmicroLife · 2024Article
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
backgroundBacteria of the candidate phyla radiation (CPR), constituting about 25% of the bacterial biodiversity, are characterized by small cell size and patchy genomes without complete key metabolic pathways, suggesting a symbiotic lifestyle. Gracilibacteria (BD1-5), which are part of the CPR branch, possess alternate coded genomes and have not yet been cultivated. The lifestyle of Gracilibacteria, their temporal dynamics, and activity in natural ecosystems, particularly in groundwater, has remained largely unexplored. Here, we aimed to investigate Gracilibacteria activity in situ and to discern their lifestyle based on expressed genes, using the metaproteogenome of Gracilibacteria as a function of time in the cold-water geyser Wallender Born in the Volcanic Eifel region in Germany.
resultsWe coupled genome-resolved metagenomics and metaproteomics to investigate a cold-water geyser microbial community enriched in Gracilibacteria across a 12-day time-series. Groundwater was collected and sequentially filtered to fraction CPR and other bacteria. Based on 725 Gbps of metagenomic data, 1129 different ribosomal protein S3 marker genes, and 751 high-quality genomes (123 population genomes after dereplication), we identified dominant bacteria belonging to Gallionellales and Gracilibacteria along with keystone microbes, which were low in genomic abundance but substantially contributing to proteomic abundance. Seven high-quality Gracilibacteria genomes showed typical limitations, such as limited amino acid or nucleotide synthesis, in their central metabolism but no co-occurrence with potential hosts. The genomes of these Gracilibacteria were encoded for a high number of proteins involved in cell to cell interaction, supporting the previously surmised host-dependent lifestyle, e.g., type IV and type II secretion system subunits, transporters, and features related to cell motility, which were also detected on protein level.
conclusionsWe here identified microbial keystone taxa in a high-CO
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