Changes in the Bacterial Community Composition of Cultivated Soil after Digging up Operations for Laying a Pipeline

Our study aimed to evaluate the impact of the pipeline installation on the bacterial composition in cultivated soil by metagenomic analyses performed before the excavation and in the following three years. Differential abundance analysis was obtained using DESeq2 from the GAIA pipeline to verify the bacteriological diversity in soils collected after the reference year (2013). Soil samples presented a different distribution of taxa, especially in 2014, in which a further allocation at the phylum and family levels was observed compared to the previous year (2013). The phyla Bacteroidetes and Firmicutes increased significantly, while the phylum Actinobacteria, most abundant in 2013, showed reduced abundance; moreover, Chloroflexi and Planctomycetes decreased considerably, and Verrucomicrobia was absent. The significant differences in the taxonomic composition and structure of the soil microbial community were due to critical stress conditions following the soil excavations. The bacterial communities were capable of profound physiological and genetic changes, implementing different mechanisms for survival and adaptation to an environment with changed conditions. The implication of changes in microbial diversity before and after the mechanical insult of soil has been determined.