Microbiome profiling of organic and conventional soil types

Conventional agriculture (CA) practices have threatened the environment over the years. The detrimental impact of conventional agriculture practices on soils could be due to negative effects on soil microbial communities. Conversely, organic agriculture (OA) practices are envisaged as potentially enhancing helpful microbial communities and are proposed as environmentally sustainable. Soil microbiome is regarded as a cornerstone influencing soil health and quality and as such, it requires deeper investigation and understanding. In this study, we compared the microbial patterns of long-term organic and conventional managed soils to explore their similarities and differences. Soil samples were collected from six farming sites in the Po River valley, Italy. Among these sites, three farms were under organic agriculture (OA) and the other three under conventional agriculture (CA). Total DNA was isolated from soil samples from each of the farms for 16S rDNA multi-amplicon sequencing, that was achieved using an Ion GeneStudio S5 System. Quantitative Real-Time PCR (qPCR) analyses were carried out to evaluate the presence of selected microbial targets including five genes covering the nitrogen cycle, as well as genes encoding for polyketide synthases (PKSs), and traits featured by plant growth-promoting bacteria (PGPB) such as those belonging to Nocardioides and Sphingomonas genera. Total DNA quantification showed an over 20-fold higher amount of DNA in OA soils (mean= 22.1±5.82 µg·g-1), compared to CA soils (mean= 0.95±0.53 µg·g-1). While the taxonomic metabarcoding evidenced the absence of significant differences among communities of the two management practices in terms of ecological indexes values, the qPCR analyses targeting functional genes reported a significantly higher abundance of targets in OA sites spanning ranges up to four-fold log increases. Each of the investigated genes, entailing different ecosystem services, was significantly more abundant in OA soils. In conclusion, while OA and CA do not appear to affect overall bacterial species diversity or evenness per se, as assessed by the metagenomics approach, on the contrary, in terms of functional diversity quantification OA showed a consistently higher abundance of all the salient microbial genes tested, when compared to CA, underlying a potentially beneficial impact on soil fertility and sustainability. In essence, the sequencing-based analysis of the absolute biodiversity cannot adequately differentiate agricultural ecosystems in relation to their managing systems hence, pairing or substituting this evaluation with the much cheaper PCR-based functional biodiversity analysis can be a suitable approach to overcome the lack of relevant information.