Nucleic Acids and Proteins in Soil
With millions of different bacterial species living in soil, the microbial community is extremely complex, varying at very small scales. Microbe-driven functions are essential for most processes in soil. Thus, a better understanding of this microbial dive
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Kaare M. Nielsen, Luca Calamai, Giacomo Pietramellara
7.1 Introduction Soils are chemically complex and spatially heterogeneous environments that offer a variety of DNA-adsorbing surfaces such as sands, silts, clays, and complex macromolecules such as humic acids and remnants of plant tissues. Different soil types vary in composition with respect to these surfaces, influencing the specific adsorption of DNA (Ladd et al. 1996). After adsorption to surfaces of quartz, feldspar, oxides or hydroxides containing heavy minerals, humic acids and clay, the DNA becomes partially resistant to degradation by extracellular nucleases (Aardema et al. 1983; Romanowski et al. 1991; Khanna and Stotzky 1992; Crecchio and Stotzky 1998). DNA fragments adsorbed on these surfaces have been shown to transform bacteria in vitro (Lorenz and Wackernagel 1990; Stewart et al. 1991; Khanna and Stotzky 1992; Paget et al. 1992; Romanowski et al. 1993; Pietramellara et al. 1997; Demanèche et al. 2001). The adsorption of DNA by soil particles is therefore important since it may extend the time period that extracellular DNA is available for natural transformation of bacterial communities (Gallori et al. 1994; Nielsen et al. 1997a,b). Table 7.1 summarises the results of studies that have examined the effects of soil particulate material and humic acids on the biological activity of DNA. These studies were carried out using purified DNA, DNA present in cell lysates from dead bacteria, or DNA naturally released from living donor bacteria (Khanna and Stotzky 1992; Gallori et al. 1994; Pietramellara et al. 1997; Nielsen et al. 2000a,b, 2004; Demanèche et al. 2001). Both prokaryotic and eukaryotic DNA have been used as sources of transforming DNA, as reviewed by Nielsen (2003) and Nielsen et al. (1998, 2001). Here, studies investigating the interaction of DNA (present in pure solution, cell lysates, and live donor cell suspensions) with soil components (present as pure substances, in mixtures, and as natural soil samples) are examined. The accessibility of adsorbed DNA Kaare M. Nielsen: Department of Pharmacy, University of Tromsø, 9037 Tromsø, Norway, E-mail: [email protected] Luca Calamai, Giacomo Pietramellara: Department of Soil Science and Plant Nutrition, University of Florence, 50144 Florence, Italy Soil Biology, Volume 8 Nucleic Acids and Proteins in Soil P. Nannipieri, K. Smalla (Eds.) © Springer-Verlag Berlin Heidelberg 2006
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Chromosomal DNA of Acinetobacter sp. incubated in a solution of humic acids
Montmorillonite
Kaolinite, ilite, montmorillonite
Chromosomal and plasmid DNA bound to clay undergoing cycles of drying and wetting
Plasmid DNA bound on clays
Sea sand Sea sand Sea sand, groundwater aquifer material
Chromosomal DNA of B. subtilis attached to sand grains
Chromosomal DNA of Pseudomonas stutzeri attached to sand grains
Plasmid and chromosomal DNA adsorbed on sand and groundwater aquifer material
Sands
Montmorillonite
Chromosomal DNA of B. subtilis adsorbed to clay
Clays
Extracted from a forest
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