Extracellular DNA in soil and sediment: fate and ecological relevance

Pietramellara, Giacomo; Ascher, Judith; Borgogni, Federica; Ceccherini, Maria Teresa; Guerri, Giulia; Nannipieri, Paolo

doi:10.1007/s00374-008-0345-8

Cited by 456 publications

(456 citation statements)

References 157 publications

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“…First, physicochemical conditions and sediment composition must be favourable to avoid the complete degradation of DNA. In Lake Anterne, sediment compounds, such as clays, sands, humic substances and organomineral complexes, that allow DNA adsorbance, together with cold temperature and periodic anoxic conditions on the lake bottom (see Methods), are likely to have favoured DNA preservation [28][29][30] . Moreover, DNA was present in all samples, even the oldest, suggesting that the DNA was sufficiently preserved to successfully reconstruct the presence of the taxa of interest.…”

Section: Discussionmentioning

confidence: 99%

Long livestock farming history and human landscape shaping revealed by lake sediment DNA

et al. 2014

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The reconstruction of human-driven, Earth-shaping dynamics is important for understanding past human/environment interactions and for helping human societies that currently face global changes. However, it is often challenging to distinguish the effects of the climate from human activities on environmental changes. Here we evaluate an approach based on DNA metabarcoding used on lake sediments to provide the first high-resolution reconstruction of plant cover and livestock farming history since the Neolithic Period. By comparing these data with a previous reconstruction of erosive event frequency, we show that the most intense erosion period was caused by deforestation and overgrazing by sheep and cowherds during the Late Iron Age and Roman Period. Tracking plants and domestic mammals using lake sediment DNA (lake sedDNA) is a new, promising method for tracing past human practices, and it provides a new outlook of the effects of anthropogenic factors on landscape-scale changes.

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Section: Discussionmentioning

confidence: 99%

Long livestock farming history and human landscape shaping revealed by lake sediment DNA

et al. 2014

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“…However, the bacterial recombinational potential with DNA should be seen in the broader context of DNA exposure. Of the vast amounts of free DNA in the environment, the majority will exhibit various stages of degradation (3,35,36). Additionally, threshold levels for biologically significant gene transfer frequencies remains to be established for bacterial systems, and differences in transfer frequencies may have little or no impact on long-term evolutionary outcomes (37).…”

Section: Discussionmentioning

confidence: 99%

“…Depurination affects the stability of the DNA backbone and leads to nicks and single-strand overhangs of the DNA fragments (2). Consequently, most free DNA fragments in the environment are <100 bp in size (3)(4)(5)(6)(7)(8). Deamination particularly affects cytosine, creating uracil residues that can lead to cytosine-tothymine exchanges, which result in DNA sequencing errors (9).…”

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confidence: 99%

Bacterial natural transformation by highly fragmented and damaged DNA

Overballe‐Petersen¹,

Harms

Orlando³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

177

142

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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, doublenucleotide 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. microbial evolution | horizontal gene transfer | DNA degradation | early life | anachronistic evolution

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“…Working with older sedimentary material, DNA degradation and fragmentation can bias the amplification success. In surface sediments that integrate both intracellular DNA of living cells and extracellular DNA (Pietramellara et al 2008), the presence of intact DNA from the living benthic community can lead to overrepresentation of these taxa in the genetic data when analysing entire communities and might lead to quantitative and qualitative differences between microscopic and genetic results. The rbcL_76 amplicon was previously shown to yield positive results in core samples and indicate turnover of species assemblages through time (Stoof-Leichsenring et al 2012).…”

Section: Usability Of Sedimentary Dna For Diatom Identification In Pamentioning

confidence: 99%

A combined paleolimnological/genetic analysis of diatoms reveals divergent evolutionary lineages of Staurosira and Staurosirella (Bacillariophyta) in Siberian lake sediments along a latitudinal transect

et al. 2014

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Diatom diversity in lakes of northwest Yakutia (Siberia) was investigated by microscopic and genetic analysis of surface and cored lake sediments, to evaluate the use of sedimentary DNA for paleolimnological diatom studies and to identify obscure genetic diversity that cannot be detected by microscopic methods. Two short (76 and 73 bp) and one longer (577 bp) fragments of the ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcL) gene, encoding the large subunit of the rbcL, were used as genetic markers. Diverse morphological assemblages of diatoms, dominated by small benthic fragilarioid taxa, were retrieved from the sediments of each lake. These minute fragilarioid taxa were examined by scanning electron microscopy, revealing diverse morphotypes in Staurosira and Staurosirella from the different lakes. Genetic analyses indicated a dominance of haplotypes that were assigned to fragilarioid taxa and less genetic diversity in other diatom taxa. The long rbcL_577 amplicon identified considerable diversification among haplotypes clustering within the Staurosira/Staurosirella genera, revealing 19 different haplotypes whose spatial distribution appears to be primarily related to the latitude of the lakes, which corresponds to a vegetation and climate gradient. Our rbcL markers are valuable tools Electronic supplementary material The online version of this article

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Extracellular DNA in soil and sediment: fate and ecological relevance

Cited by 456 publications

References 157 publications

Long livestock farming history and human landscape shaping revealed by lake sediment DNA

Long livestock farming history and human landscape shaping revealed by lake sediment DNA

Bacterial natural transformation by highly fragmented and damaged DNA

A combined paleolimnological/genetic analysis of diatoms reveals divergent evolutionary lineages of Staurosira and Staurosirella (Bacillariophyta) in Siberian lake sediments along a latitudinal transect

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