Bacterial Microbiota and Soil Fertility of Crocus sativus L. Rhizosphere in the Presence and Absence of Fusarium spp.

Abstract

Intensive agricultural practices have led to intense soil degradation and soil fertility losses. Many soil-borne diseases affect these intensive agricultural soils, worsening the physical-chemical and fertility imbalances. Among the numerous pathogens, the genus Fusarium includes members that destroy many crops, including Crocus sativus L., which also impairs the composition and functions of the microbial communities. This work aimed to investigate, for the first time, the bacterial communities of the rhizosphere of saffron in the presence and absence of fusariosis. The rhizosphere of the saffron fields in the territory of L’Aquila (Italy) with and without fusariosis was sampled and subjected to a microbiological analysis. Culture-dependent methods characterized the fusariosis. The dehydrogenase activity assay was estimated. The metabarcoding of the 16S rRNA gene, a metagenome functioning prediction, and a network analysis were also carried out. The results showed that fusariosis, when it is linked to intensive agricultural practices, causes alterations in the microbial communities of the rhizosphere. The culture-dependent and independent approaches have shown changes in the bacterial community in the presence of fusariosis, with functional and enzymatic imbalances. The samples showed a prevalence of uncultured and unknown taxa. Most of the known Amplicon Sequence Variants (ASVs) were associated with the Pseudomonadoa (syn. Proteobacteria) lineage. The composition and richness of this phylum were significantly altered by the presence of Fusarium. Moreover, pathogenesis appeared to improve the ASVs interconnections. The metagenome functions were also modified in the presence of fusariosis.