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DNA molecules are continuously released through decomposition of organic matter and are ubiquitous in most environments. Such DNA becomes fragmented and damaged (often <100 bp) and may persist in the environment for more than half a million years. Fragmented DNA is recognized as nutrient source for microbes, but not as potential substrate for bacterial evolution. Here, we show that fragmented DNA molecules (≥ 20 bp) that additionally may contain abasic sites, cross-links, or miscoding lesions are acquired by the environmental bacterium Acinetobacter baylyi through natural transformation. With uptake of DNA from a 43,000-y-old woolly mammoth bone, we further demonstrate that such natural transformation events include ancient DNA molecules. We find that the DNA recombination is RecA recombinase independent and is directly linked to DNA replication. We show that the adjacent nucleotide variations generated by uptake of short DNA fragments escape mismatch repair. Moreover, double-nucleotide polymorphisms appear more common among genomes of transformable than nontransformable bacteria. Our findings reveal that short and damaged, including truly ancient, DNA molecules, which are present in large quantities in the environment, can be acquired by bacteria through natural transformation. Our findings open for the possibility that natural genetic exchange can occur with DNA up to several hundreds of thousands years old.

Original publication

DOI

10.1073/pnas.1315278110

Type

Journal article

Journal

Proceedings of the national academy of sciences of the united states of america

Publication Date

12/2013

Volume

110

Pages

19860 - 19865

Addresses

Centre for GeoGenetics and Nordic Center for Earth Evolution, University of Copenhagen, 1350 Copenhagen K, Denmark.

Keywords

Animals, Acinetobacter, DNA Damage, DNA, DNA Primers, Transformation, Bacterial, Sequence Analysis, DNA, Evolution, Molecular, Gene Transfer, Horizontal, Base Sequence, Molecular Sequence Data, Mammoths