Articles
A novel aptamer-based approach for detecting a target microorganism in soil
Article number
1427_21
Pages
163 – 168
Language
English
Abstract
The uncertainty associated with the impact of a bioinoculant on soil microbial community and, as a consequence, on soil quality, as well as the need to define its persistence, has prompted the demand for an accurate detection and tracking system of the presence and the quantification of a target microbial inoculant in soil.
Although DNA or RNA-based molecular detection are well established and commonly applied in this regard, alternative ligands such as DNA-aptamers have several advantages over them, such as low cost, ease of modification, ease of immobilisation on lab-on-chip or nanosensors, high chemical and thermal stability.
In this study, we used a toggle-cell SELEX method to isolate, select and characterize ssDNA (single-strand DNA) aptamers to detect a Bacillus subtilis strain which is being tested as a plant growth-promoting rhizobacteria (PGPR) formulation.
Two ssDNA aptamers (patent application n.102022000022590) showed strong affinity and specificity for B. subtilis strains, with values of the kinetic parameters Kd (dissociation constant) and Bmax (maximum intensity of binding) in the nanomolar range and around 1, respectively.
Aptamers suitability was validated on three inoculated soils characterized by different chemical-physical features and in soil from a field trial with the formulated B. subtilis PCM/B 00105 strain.
Aptamers proved to be an efficient tool to monitor a strain-specific bacteria in soil, applicable in the optimisation of bioinoculants use and suitable to support the registration processes of these products.
Although DNA or RNA-based molecular detection are well established and commonly applied in this regard, alternative ligands such as DNA-aptamers have several advantages over them, such as low cost, ease of modification, ease of immobilisation on lab-on-chip or nanosensors, high chemical and thermal stability.
In this study, we used a toggle-cell SELEX method to isolate, select and characterize ssDNA (single-strand DNA) aptamers to detect a Bacillus subtilis strain which is being tested as a plant growth-promoting rhizobacteria (PGPR) formulation.
Two ssDNA aptamers (patent application n.102022000022590) showed strong affinity and specificity for B. subtilis strains, with values of the kinetic parameters Kd (dissociation constant) and Bmax (maximum intensity of binding) in the nanomolar range and around 1, respectively.
Aptamers suitability was validated on three inoculated soils characterized by different chemical-physical features and in soil from a field trial with the formulated B. subtilis PCM/B 00105 strain.
Aptamers proved to be an efficient tool to monitor a strain-specific bacteria in soil, applicable in the optimisation of bioinoculants use and suitable to support the registration processes of these products.
Publication
Authors
A. Manfredini, E. Malusà, L. Canfora
Keywords
DNA aptamer, B. subtilis, detection, soil
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