ArticleEnvironmental microbiome2024
Genome streamlining in Parcubacteria transitioning from soil to groundwater.
Article in Environmental microbiome, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Microbial ecology of shallow groundwater ecosystems.Nature reviews. Microbiology · 2026Review
- Groundwater microbial communities across the terrestrial subsurface.Nature microbiology · 2026Review
- Exploring microbial diversity using cell-size fractionated enrichment incubations from subsurface aquifers at Äspö, Sweden.Communications biology · 2026Article
- Diversity and ecological roles of hidden viral players in groundwater microbiomes.Nature communications · 2026Article
- Candidate Phyla Radiation (CPR) bacteria from hyperalkaline ecosystems provide novel insight into their symbiotic lifestyle and ecological implications.Microbiome · 2025Article
- Proteomic evidence for aerobic methane production in groundwater by methylotrophic Methylotenera.The ISME journal · 2025Article
- Alkane degradation mechanism ofFrontiers in microbiology · 2025Article
- Carbon and microbes in a degrading palsa mire are distinct from a peatland and a wider connected sub-Arctic fluvial system.ISME communications · 2025Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTo 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.
resultsBacterial 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.
conclusionsOverall, 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.
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