Genome streamlining in Parcubacteria transitioning from soil to groundwater.

Autor: Chaudhari NM; Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.; German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Friedrich-Schiller-Universität, Leipzig, Germany., Pérez-Carrascal OM; Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany., Overholt WA; Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany., Totsche KU; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.; Hydrogeology, Institute of Geowissenschaften, Friedrich-Schiller-Universität Jena, Burgweg 11, 07749, Jena, Germany., Küsel K; Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany. kirsten.kuesel@uni-jena.de.; German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Friedrich-Schiller-Universität, Leipzig, Germany. kirsten.kuesel@uni-jena.de.; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany. kirsten.kuesel@uni-jena.de.
Jazyk: angličtina
Zdroj: Environmental microbiome [Environ Microbiome] 2024 Jun 20; Vol. 19 (1), pp. 41. Date of Electronic Publication: 2024 Jun 20.
DOI: 10.1186/s40793-024-00581-6
Abstrakt: Background: To better understand the influence of habitat on the genetic content of bacteria, with a focus on members of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil via seepage waters to groundwater on genomic composition of ultra-small Parcubacteria, the dominating CPR class in seepage waters, using genome resolved metagenomics.
Results: Bacterial metagenome-assembled genomes (MAGs), (318 total, 32 of Parcubacteria) were generated from seepage waters and compared directly to groundwater counterparts. The estimated average genome sizes of members of major phyla Proteobacteria, Bacteroidota and Cand. Patescibacteria (Candidate Phyla Radiation - CPR bacteria) were significantly higher in soil-seepage water as compared to their groundwater counterparts. Seepage water Parcubacteria (Paceibacteria) exhibited 1.18-fold greater mean genome size and 2-fold lower mean proportion of pseudogenes than those in groundwater. Bacteroidota and Proteobacteria also showed a similar trend of reduced genomes in groundwater compared to seepage. While exploring gene loss and adaptive gains in closely related CPR lineages in groundwater, we identified a membrane protein, and a lipoglycopeptide resistance gene unique to a seepage Parcubacterium genome. A nitrite reductase gene was also identified and was unique to the groundwater Parcubacteria genomes, likely acquired from other planktonic microbes via horizontal gene transfer.
Conclusions: Overall, our data suggest that bacteria in seepage waters, including ultra-small Parcubacteria, have significantly larger genomes and higher metabolic enrichment than their groundwater counterparts, highlighting possible genome streamlining of the latter in response to habitat selection in an oligotrophic environment.
(© 2024. The Author(s).)
Databáze: MEDLINE
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