Cultivation type, season, and soil nematode interactions affect wheat rhizosphere metabarcoding profiles

The aim of this study was the evaluation of bacterial profiles and diversity in the rhizosphere of durum wheat, Triticum turgidum subsp. durum, in two different crop management types (organic vs. conventional) and at two sampling times. We investigated the links of rhizosphere bacteria with crop management and other variables, including soil nematodes and physicochemical profiles.

Metabarcoding samplings were carried out in organic and conventional durum wheat fields at Gravina (Italy), before (March) and after (May) heading, including adjacent uncultivated controls. Bacterial amplicon sequence variants (ASVs) were obtained by RNA extraction from rhizosphere soil, followed by NGS sequencing of the V3-V4 regions of the 16S rRNA ribosomal gene. The nematodes were classified as herbivores, fungivores/moss feeders, bacterivores, and omnivores/predatory.

Crop fertilization and sampling time were effective drivers interacting with soil physicochemical traits and nematode guilds. Spearman's correlation showed, in March, an inverse relationship of herbivores with all other guilds. In May, the herbivores were inversely correlated with the fungal/moss feeders. The sampling season affected the correlations among nematode guilds as well as ASV profiles, in both the control and cultivated samples. ASV diversity indexes did not vary significantly among treatments, except for the Menhinick index in the organic wheat control. In general, a shift toward a richer ASV metabarcoding profile was observed in May for both crop types, with a higher diversity and abundance in the organic wheat. Crop management type, sampling time, and soil physicochemical properties significantly affected the rhizosphere microbiota, with Alphaproteobacteria (Methylobacteriaceae and Sphingomonadaceae) as the most represented in both wheat crops. Positive or inverse correlations linked nematode groups and ASV, with profiles almost specific for each guild. Bacteria inversely correlated with herbivores included Bacillus sp., Methylorubrum sp., uncl. Lactobacillales, Cyanobacteria, and other taxa. Positive correlations included plant growth promoters and bacteria involved in N₂ and nutrient cycling.

The ASV profiles differed by management type and sampling time, as the sampling season affected the bacterial community, with the organic wheat always characterized by a higher richness and service redundancy. The occurrence of bacteria selectively associated with each nematode guild suggests the presence of multiple functional services deployed at the nematode-bacteria-rhizosphere interface.