Adsorption capacity of multiple DNA sources to clay minerals and environmental soil matrices less than previously estimated

Abstract

The cultivation and consumption of transgenic crops continues to be a widely debated topic, as the potential ecological impacts are not fully understood. In particular, because antibiotic resistance genes (ARGs) have historically been used as selectable markers in the genetic engineering of transgenic crops, it is important to determine if the genetic constructs found in decomposing transgenic crops persist long enough in the environment and if they can be transferred horizontally to indigenous microorganisms. In the present study, we address the question of persistence. Others have also estimated the DNA adsorption capacity of various clays, but have done so by manipulating the surface charge and size of particles tested which may overestimate sorption and underestimate the DNA available for horizontal transfer. In the present study, isotherms were generated using model Calf Thymus DNA and transgenic maize DNA without surface modification. Montmorillonite, kaolinite, and 3 soil mixtures with varying clay content were used in this study. The adsorption capacity of pure montmorillonite and kaolinite minerals was found to be one to two orders of magnitude less than previously estimated likely due to the distribution of clay particle sizes and heteroionic particle surface charge. However, it appears that a substantial amount of DNA is still able to adsorb onto these matrices (up to 200 mg DNA per gram of clay) suggesting the potential availability of free transgenic DNA in the environment may still be significant. Future studies should be conducted to determine the fate of these genes in agricultural soils.

Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

“…Many of the factors that in uence PMA effectiveness have been well-explored in previous studies. In soil samples, for example, the mineralogy, pH, and ionic conditions all in uence the longevity of relic DNA via adsorption of DNA molecules to soil matrices [2,19], sequestering it from PMA intercalation [19,20]. This was re ected in our own soil data and its comparison to previous studies by the relatively small effects of PMA on any microbes (Fig.…”

Examining the behavior of crop‐derived antibiotic resistance genes in anaerobic sludge batch reactors under thermophilic conditions

“…This association between DNA sequence length and environmental persistence has been noted in several other environments (Nielsen, Johnsen, Bensasson, & Daffonchio, ; Ogram, Sayler, Gustin, & Lewis, ; Pietramellara, Ascher, Ceccherini, Nannipieri, & Wenderoth, ), though this is the first study to confirm this trend in reactors mimicking WWTP anaerobic digestion. DNA adsorption to clay particles and organic matter further increases this protection and has been noted in several other environments (Gardner & Gunsch, ; Mao et al, ). Adsorption may explain the persistence of eDNA in the control reactors and suggest a novel potential source for ARG dissemination in WWTPs.…”

“…Consumption of transgenic crops and crop by‐products is common in the United States. Historically, several lines of transgenic or genetically engineered (GE) crops have incorporated one or more antibiotic resistance genes (ARGs) including β‐lactamase (e.g., bla ) and neomycin (e.g., nptII ) resistance genes (Bennett et al, ; Conner, Glare, & Nap, ; Dunfield & Germida, ; Gardner & Gunsch, ; Iamtham & Day, ). While these genes are less frequently incorporated into GE crops in the United States, ARGs are still used in some transgenic crops consumed in lower resourced countries and were once used in GE crops in North America due to their ease of use during the plant transformation process (ISAAA, ).…”

Preliminary evidences of the presence of extracellular DNA single stranded forms in soil

“…All these functions and peculiar traits make eDNA to one of the most interesting molecules in soil, capable to affect both the composition and activity of microbial and plant communities. However, despite the increasing evidences on multiple roles and functions of eDNA in soil, the discrimination between its single and double stranded fractions has been up to now neglected although they are characterized by different reactivity and adsorption capacity [19,20,21]. To the best of our knowledge, there are only few studies dealing with eDNAss with focus on its adsorption onto clays [19,21] and other minerals [22] under laboratory conditions.…”

“…However, despite the increasing evidences on multiple roles and functions of eDNA in soil, the discrimination between its single and double stranded fractions has been up to now neglected although they are characterized by different reactivity and adsorption capacity [19,20,21]. To the best of our knowledge, there are only few studies dealing with eDNAss with focus on its adsorption onto clays [19,21] and other minerals [22] under laboratory conditions. Thus, the present study aimed to assess the most mobile fraction of soil eDNA, based on the sequential extraction method by Ascher et al [1], that is capable to specifically evaluate and characterize the eDNA fractions that are weakly (adsorbed) and strongly bound onto soil colloids, thus discriminating between the DNA forms with high and low mobility in soil.…”