Pseudomonas putida isolation and quantification by real-time pcr in agricultural soil biodegradable mulching

Abstract

To reduce the plastic waste problem in agriculture, biodegradable plastic (BP) mulch films have become of key importance thanks to their biodegradability and beneficial effects on crops. However, at present, BPs cannot always replace conventional plastics, because biodegradation is governed by many biotic and abiotic factors under field conditions. This research aimed at isolating and identifying, from soil particles directly attached to the surface of BP samples, the microorganisms responsible of degradation through a combined approach based on biodegradation and molecular tests. For this purpose, a field trial within a Mediterranean apricot orchard was carried out to study the biodegradation of a commercial BP mulch with respect to a no-BP, a conventional apricot management, following the standard agricultural practices, and a subterranean clover cover cropping, either incorporating or leaving its dead mulches on the soil surface. After BP film appeared visibly degraded in field, we isolated from soil particles attached to the polymer surface, a mesophilic bacterium with certain degradative potential assessed by plate and liquid assays, identified by sequencing as Pseudomonas putida. Quantitative real time PCR analysis showed the P. putida was significantly more abundant in PB plots than the other plot treatments. These preliminary results are potentially applicable to accelerate the degradation of BP mulch films and decrease the plastic pollution in agriculture.