Comparative Analysis of Perennial and Annual Rice: Biochemical Composition, Soil Microbiological Diversity, and Agrochemical Characteristics Under the Conditions of Kazakhstan

This study aimed to comparatively evaluate the physicochemical and biochemical properties of grain and straw from annual and perennial rice cultivated under different soil–climatic conditions in the Kyzylorda and Almaty regions of Kazakhstan, and to investigate the microbiological and agrochemical characteristics of associated rice field soils. The experimental materials included grain, straw, and soil samples collected at full maturity from field trials. Standard analytical procedures were applied, including Kjeldahl nitrogen determination, moisture content analysis, crude fiber assessment, microbiological culturing using serial dilution techniques on selective media, and agrochemical analysis of soil organic carbon, nitrogen, phosphorus, potassium, and humus content. The results demonstrated significant variation in grain composition depending on both cultivation system and geographic location. Perennial rice consistently exhibited higher protein content (4.73–4.90%) compared to annual rice (3.56–3.84%), while showing reduced moisture (9.58–9.72% vs. 12.36–13.62%) and lower crude fiber content. These differences suggest enhanced nitrogen assimilation efficiency and improved grain quality in perennial rice systems. Microbiological analysis revealed significantly greater abundance and diversity of aerobic and functional microorganisms in soils cultivated with perennial rice than in annual rice and non-cultivated control soils. The total number of aerobic microorganisms reached 820.5 × 103 and 175.2 × 103 CFU mL−1 in perennial rice soils, whereas control soils contained only 55.3 × 103 and 81.7 × 103 CFU mL−1. The highest abundance of phosphate-solubilizing microorganisms was recorded in the perennial rice field in the Almaty region (2.32 × 109 CFU g−1 soil), indicating the formation of highly active microbial communities involved in phosphorus mobilization and nutrient cycling. Agrochemical analyses further showed that perennial rice promoted the accumulation of soil organic carbon, nitrogen, and humus following topsoil removal, with total organic carbon reaching 1.68% compared with only 0.43% in soils without perennial rice. These findings suggest that the extensive root system of perennial rice contributes to enhanced carbon sequestration and improved soil fertility. Overall, perennial rice demonstrated favorable physicochemical, biochemical, microbiological, and agrochemical characteristics, including improved nutrient composition, enhanced microbial diversity, greater abundance of beneficial phosphate-solubilizing bacteria, and increased accumulation of soil organic matter. The findings highlight the potential of perennial rice as a sustainable agricultural system capable of improving grain quality while promoting long-term soil fertility, microbial biodiversity, and ecosystem stability under the conditions of Kazakhstan.