ArticleFrontiers in microbiology2015
Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population.
Article in Frontiers in microbiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 71 citations in OpenAlex.
- Depth-resolved transcriptional activity of antibiotic resistance genes in deep permafrost of the Qinghai-Tibet Plateau.Communications biology · 2026Article
- Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes.Nature microbiology · 2025Article
- Single cell viral tagging ofGut microbes · 2025Article
- Subsurface Life on Earth as a Key to Unlock Extraterrestrial Mysteries.Microbial biotechnology · 2025Review
- Virolithopanspermia: Might viruses be transported in rocks through space?PLoS pathogens · 2025Article
- A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide.Science advances · 2024Article
- Microbial ecology of the deep terrestrial subsurface.The ISME journal · 2024Review
- Coexistence of Psychrophilic, Mesophilic, and Thermophilic Sulfate-Reducing Bacteria in a Deep Subsurface Aquifer Associated with Coal-Bed Methane Production.Microbial ecology · 2023Article
- The smallest in the deepest: the enigmatic role of viruses in the deep biosphere.National science review · 2023Review
- Back to Basics: A Simplified Improvement to Multiple Displacement Amplification for Microbial Single-Cell Genomics.International journal of molecular sciences · 2023Article
- Towards an integrative view of virus phenotypes.Nature reviews. Microbiology · 2022Review
- Advances in Defining Ecosystem Functions of the Terrestrial Subsurface Biosphere.Frontiers in microbiology · 2022Review
- Evolutionary stasis of a deep subsurface microbial lineage.The ISME journal · 2021Article
- Tracking Microbial Evolution in the Subseafloor Biosphere.mSystems · 2021Article
- Lytic archaeal viruses infect abundant primary producers in Earth's crust.Nature communications · 2021Article
- Examining horizontal gene transfer in microbial communities.Nature reviews. Microbiology · 2021Review
- Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation.The ISME journal · 2021Article
- The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles.Communications biology · 2021Article
- Insights into the dynamics between viruses and their hosts in a hot spring microbial mat.The ISME journal · 2020Article
- Microbial single-cell omics: the crux of the matter.Applied microbiology and biotechnology · 2020Review
Corrections and comments
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Authors and funding
9 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A major fraction of Earth's prokaryotic biomass dwells in the deep subsurface, where cellular abundances per volume of sample are lower, metabolism is slower, and generation times are longer than those in surface terrestrial and marine environments. How these conditions impact biotic interactions and evolutionary processes is largely unknown. Here we employed single cell genomics to analyze cell-to-cell genome content variability and signatures of horizontal gene transfer (HGT) and viral infections in five cells of Candidatus Desulforudis audaxviator, which were collected from a 3 km-deep fracture water in the 2.9 Ga-old Witwatersrand Basin of South Africa. Between 0 and 32% of genes recovered from single cells were not present in the original, metagenomic assembly of Desulforudis, which was obtained from a neighboring subsurface fracture. We found a transposable prophage, a retron, multiple clustered regularly interspaced short palindromic repeats (CRISPRs) and restriction-modification systems, and an unusually high frequency of transposases in the analyzed single cell genomes. This indicates that recombination, HGT and viral infections are prevalent evolutionary events in the studied population of microorganisms inhabiting a highly stable deep subsurface environment.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.