Assessment of Bacterial Diversity and Rhizospheric Community Shifts in Maize (Zea mays L.) Grown in Soils with Contrasting Productivity Levels

The resident microbiota in agricultural soils strongly influences crop health and productivity. In this study, we evaluated the prokaryotic diversity of two clay soils with similar physicochemical characteristics but contrasting levels of maize (<i>Zea mays</i> L.) and wheat (<i>Triticum aestivum</i> L.) production using 16S rRNA gene sequencing. Yield records showed significant differences in grain production over five consecutive years. When comparing prokaryotic alpha diversity between the "non-productive" and "productive" soils, no major differences were found, and the abundance of ammonia-oxidizing archaea (AOA) and bacterial genera such as <i>Arthrobacter</i>, <i>Neobacillus</i>, and <i>Microvirga</i> remained consistent across soils. Analysis of the top 20 genera showing the greatest abundance shifts by compartment (bulk soil vs. rhizosphere) revealed that genera such as <i>Priestia</i>, <i>Neobacillus</i>, <i>Sporosarcina</i>, and <i>Pontibacter</i> decreased in the rhizosphere of the non-productive soil, while in the productive soil, these genera remained unchanged. In the non-productive soil, genera such as <i>Flavisobacter</i> decreased in abundance in the rhizosphere, whereas <i>Arthrobacter</i> increased. Principal coordinates analysis (PCoA) showed no clear clustering by compartment (bulk vs. rhizosphere), but two distinct clusters emerged when grouping by soil type (productive vs. non-productive). Interaction networks varied by soil type: non-productive soils showed positive <i>Candidatus</i>-<i>Bacillus</i> and negative <i>Massilia</i> links, while productive soils were dominated by <i>Flavisolibacter</i> and negative <i>Pontibacter</i>. Across soils, <i>Rhizobium</i>-<i>Bradyrhizobium</i> associations were positive, whereas <i>Neobacillus</i> and <i>Priestia</i> were negative. These findings highlight that a few potential beneficial microbiota and their interactions may be key drivers of soil productivity, representing targets for microbiome-based agricultural management.