Release and persistence of extracellular DNA in the environment

Abstract

The introduction of genetically modified organisms (GMOs) has called for an improved understanding of the fate of DNA in various environments, because extracellular DNA may also be important for transferring genetic information between individuals and species. Accumulating nucleotide sequence data suggest that acquisition of foreign DNA by horizontal gene transfer (HGT) is of considerable importance in bacterial evolution. The uptake of extracellular DNA by natural transformation is one of several ways bacteria can acquire new genetic information given sufficient size, concentration and integrity of the DNA. We review studies on the release, breakdown and persistence of bacterial and plant DNA in soil, sediment and water, with a focus on the accessibility of the extracellular nucleic acids as substrate for competent bacteria. DNA fragments often persist over time in many environments, thereby facilitating their detection and characterization. Nevertheless, the long-term physical persistence of DNA fragments of limited size observed by PCR and Southern hybridization often contrasts with the short-term availability of extracellular DNA to competent bacteria studied in microcosms. The main factors leading to breakdown of extracellular DNA are presented. There is a need for improved methods for accurately determining the degradation routes and the persistence, integrity and potential for horizontal transfer of DNA released from various organisms throughout their lifecycles.

Bacterial natural transformation by highly fragmented and damaged DNA

“…Our findings open for the possibility that natural genetic exchange can occur with DNA up to several hundreds of thousands years old. microbial evolution | horizontal gene transfer | DNA degradation | early life | anachronistic evolution D NA molecules are continuously released into the surroundings through decomposition of organic matter and are ubiquitous in most environments (1). DNA degradation is initiated at cell death by coreleased cellular nucleases and continued by microbes feeding on organic matter (1).…”

“…microbial evolution | horizontal gene transfer | DNA degradation | early life | anachronistic evolution D NA molecules are continuously released into the surroundings through decomposition of organic matter and are ubiquitous in most environments (1). DNA degradation is initiated at cell death by coreleased cellular nucleases and continued by microbes feeding on organic matter (1). Because fragmentation proceeds quickly, larger (gene-length) fragments are not expected to persist in the environment (1).…”

“…DNA degradation is initiated at cell death by coreleased cellular nucleases and continued by microbes feeding on organic matter (1). Because fragmentation proceeds quickly, larger (gene-length) fragments are not expected to persist in the environment (1). Extracellular DNA is further modified by spontaneous biochemical, chemical, or physical processes, of which the most important are hydrolysis and oxidation (2).…”

Risks from GMOs due to Horizontal Gene Transfer

“…However, this rate of transformation is likely to be much greater than what would be possible in natural environments where the persistence of DNA in a transformable state and availability of suitable competent bacteria is expected to be much lower (Nielsen et al, 2007;Simpson et al, 2007).…”

“…Nevertheless, most gene transfers between multicellular eukaryotes and other organisms are detected over time scales of millions of years. This is despite the abundant availability of genetic material in living organisms, and externally, such as in soil, water, feces or even processed foods (Brinkmann and Tebbe, 2007;Douville et al, 2007;Kharazmi et al, 2003;Nielsen et al, 2007). Only a few types of HGT occur sufficiently often to be observed.…”