*2.4. Methodology of Chemical and Physicochemical Analyses of Soil*

Fraction size of soil from cultivation of winter wheat, winter rape, and field pea was measured using a Malvern Mastersizer 2000 Laser Diffraction. The physicochemical analyses included the determination of soil pH in 1 mol KCl dm−<sup>3</sup> [54], hydrolytic acidity (HAC), and the sum of exchangeable base cations (EBC) according to the method outlined by Carter and Gregorich [55], whereas the chemical analyses included the determination of organic carbon content according to the method outlined by Tiurin [56], total nitrogen content according to the method outlined by Kjeldahl [57], available phosphorus and potassium contents according to the method outlined by Egner et al. [58], magnesium content with the atomic absorption spectrometry (AAS) according to the method outlined by Schlichting et al. [59], and exchangeable cations, K+, Ca2+, Mg2+, and Na<sup>+</sup> according to the ISO 11260 [60] procedure. Determinations were carried out in the following solutions: HAC in 1 mol (CH3COO)2Ca dm<sup>−</sup>3, EBC in 0.1 mol HCl dm−3; organic carbon in a mixture of 0.13 mol K2Cr2O7 and concentrated H2SO4 in the ratio of 1,1; total nitrogen—wet mineralization in concentrated H2SO4; available phosphorus and potassium in a mixture of 0.03 (CH3CHOHCOO)2Ca·H2O and 0.02 mol HCl; magnesium in 0.012 mol CaCl2·6H2O; and exchangeable cations: K<sup>+</sup>, Ca2<sup>+</sup>, Mg2+, and Na<sup>+</sup> in 1 mol CH3COONH4.

## *2.5. Statistical Analysis*

Counts of microorganisms, the activity of soil enzymes, and the physicochemical and chemical properties of soil were developed statistically using the Statistica 13.1 package (StatSoft, Tulsa, OK, USA) [61]. The results were compared with ANOVA and then with a post hoc Tukey test (HSD). Homogenous groups were computed at *p* = 0.05. The data meet assumptions of normality and similar

variance. Analyses of metagenomic profiles were performed on the STAMP 2.1.3. software (Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia) [62] and the Circos 0.68 package (Canada's Michael Smith Genome Sciences Center, Vancouver, British Columbia V5Z 4S6, Canada) [63]. The abundance of each family and genus is directly proportional to the width of each band connecting bacterial taxa with an appropriate soil sample from the cultivation of: B—*Brassica napus*, T—*Triticum aestivum*, and P—*Pisum sativum* ssp. *arvense*. A specified color is assigned to each family and genus of bacteria. The outer ring represents the total percentage of 16S sequences, whereas the inner ring represents the number of 16S amplicon sequences assigned to a given taxon.

The relative abundance of bacteria was calculated using a two-sided test of statistical hypotheses, i.e., the G-test (w/Yates') + Fisher's, with the method of intervals confidence Asymptotic with CC [62]. The relative abundance of bacteria was visualized with the use of sequences whose percentage contribution was higher than 1%.

## **3. Results**
