Ecological Diversity of Bacterial Rhizomicrobiome Core during the Growth of Selected Wheat Cultivars

SIMPLE SUMMARY: The rhizosphere is the narrow region of soil that is directly influenced by root secretions and their associated microorganisms, named as the root microbiome. The rhizosphere is known as the niche most rich in microorganisms. From a microbiological point of view, the identification of these microorganisms and the discovery of the functions they perform by living, for example, in symbiosis with plants, is of interest. Consequently, this study aims to analyze the diversity of soil bacteria inhabiting the rhizospheric zone of wheat (Triticum aestivum L.), represented by four wheat cultivars (Tytanika, Nordcap, Hondia, Rotax), employing three methods of microbiome determination: (1) membership, (2) composition, and (3) functionality. Wheat cultivation in Poland is cropped on about 20% of all arable land. The studied cultivars are characterized by good yielding parameters and are highly popular for growing in Poland. A technique independent of cultivation (NGS—Next Generation Sequencing) was applied for microbial biodiversity determination, whereas for prediction of their ecological functionality, the FAPROTAX database was utilized. By performing lab analyses, we evidenced that molecular identification of the core rhizomicrobiome is particularly important for understanding the general principles regarding the selection of microorganisms around living roots and for harnessing the power of the microbiome in agricultural practice. ABSTRACT: One of the latest ecological concepts is the occurrence of a biased rhizosphere of microorganisms recruited mostly through interactions among various components of the rhizosphere, including plant roots and the bulk soil microbiome. We compared the diverse attributes of the core microbiome of wheat rhizosphere communities with wheat (W) and legume (L) forecrops determined by three different methods in this study (membership, composition, and functionality). The conclusions of the three methods of microbiome core definition suggest the presence of generalists, i.e., some representative microorganisms from Proteobacteria, Actinobacteria, Hypomicrobiaceae, Bradyrhizobiaceae, Sphingomonas sp., in the wheat rhizomicrobiome. The relative abundance of the core microbiome accounted for 0.1976% (W) and 0.334% (L)—membership method and 6.425% (W) and 4.253% (L)—composition method. Additionally, bacteria of the specialist group, such as Rhodoplanes sp., are functionally important in the rhizomicrobiome core. This small community is strongly connected with other microbes and is essential for maintenance of the sustainability of certain metabolic pathways.