Understanding soil–plant–microbe inter- and intra- interactions are essential for ensuring proper soil health, quality, and soil-mediated ecosystem services (e.g., nutrient cycling) required for human–plant–animal life. Intensive and unsustainable farming practices can decrease soil microbial biodiversity, fertility, and quality leading to soil degradation, impaired nutrient cycling, and the incapability of soil to support plant growth. Under such a context, soil biological fertility can appear as a regenerative component that has the potential to harmonize and improve soil’s physical, chemical, and biological parameters. This study defines and discusses the microbiome in the rhizosphere, microbial nutrient cycling, and biological soil crusts as the major components of soil biological fertility, and explores the answers to the following questions: (i) how does the rhizosphere promote plant growth, development, and nutrient cycling through soil microorganisms (e.g., bacteria, fungi)? (ii) How can soil microorganisms regulate macronutrient cycling and facilitate biocrust formation? This review reveals that soil biological fertility is crucial for increasing crop resilience and productivity as well as sustainability in agriculture. Additionally, the reintroduction of plant growth promoting rhizobacteria, a quantitative estimation of the root exudate’s composition, identifying the spatiotemporal dynamics of potassium solubilizing bacteria and establishing biological soil crusts in agricultural lands remain the major tasks for improving soil biological fertility and the transition towards regenerative agriculture.

Endophytes are associated with host plants throughout their life history from seed germination to fruit development. One of the most important plant organs colonized by endophytic microbiota is the seed. The aim of this study was to determine the structure of the seed core microbiome inhabiting the endosperms and embryos of eight wheat cultivars with the use of a culture-independent technique. The seeds of Triticum aestivum L. cv. Hondia, Wilejka, STH, Opcja, Tybalt, Euforia and Triticum spelta L. cv. Rokosz and Schwabencorn (producer: Plant Breeding Strzelce Sp. z o.o. Group IHAR) were studied. Rokosz and Hondia were cultured in vitro and in vivo to identify obligatory bacterial endophytes. A restrictive analysis of reads originating from the in vitro plants has demonstrated that the bacterial genera Paenibacillus and Propionibacterium inhabiting Rokosz and Hondia plants have a status of obligatory microorganisms. Greater biodiversity of seed-borne endophytes was found in the seed endosperms than in the embryos. The multiple comparison analysis of the OTU abundance indicated that the seed part significantly influenced the relative abundance. The seed-born microbiome is not statistically significantly dependent on the wheat cultivars; however, it cannot be claimed that every wheat seed is the same.

Comparative studies, such as the analysis of physicochemical properties and the microbiological composition of soil, are burdened with many problems resulting from the various locations of soils—often, different weather conditions among the experimental fields and varying time between the sample collection and analysis. The aim of this study was to assess the differences in the physiological profiles of bacterial communities from eight different types of soils from Poland, used in the microplot experiment that was established in 1881. The same plant species were continuously grown at all plots, at the same time, and the soil received the same type of fertilization. Moreover, the soils were always under the same weather conditions. The community-level physiological profiles of microorganisms were evaluated by using the Biolog EcoPlate™ method. The analysis demonstrated that good quality soils, especially the Gleyic Chernozem, Cambic Leptosol, and the Fluvic Cambisol exhibit a significantly higher enzyme activity, compared with the dystric soils. The dehydrogenases activity in the different time-points indicates a wide soil microbiome buffering capacity, which allows the persistence of a relatively permanent physiological profile, over many years.

Soil is an ecosystem capable of producing the resources necessary for the development of the living organisms. Soil microorganisms (bacteria and fungi) are responsible for biomass decomposition, biogenic element circulation, which makes nutrients available to plants, biodegradation of impurities, and maintenance of soil structure. The presence of microorganisms in soil depends on their chemical composition, moisture, pH, and structure. Human activity has an indispensable influence on the formation of ecosystems. Soil tillage has an impact on the chemical and physical parameters of the soil, and thus on its biological properties. The use of inappropriate agro-technology can lead to degradation of the soil environment. Changes in soil properties may cause changes in soil abundance, activity, and diversity. Cultivation can affect microorganisms, causing their mortality and reducing the availability of nourishment in the soil. Therefore, it is extremely important to assess the diversity and microbiological activity of soil in relation to soil-tillage technology.