Organic fertilizer substitution over six years improves the productivity of garlic, bacterial diversity, and microbial communities network complexity

The replacement of chemical fertilizer with organic fertilizer has been shown to boost soil fertility and crop yield. However, there is limited information on fertilization schemes suitable for sustainable production in rice-broad bean-rice-garlic rotation system. The goal of this research was to explore the transformations in microbial community compositions and networks under different types of fertilization in the garlic season with a reasonable fertilization, leading to determine the best fertilization scheme suitable for long-term deployment of garlic season. A long-term field test (2015–2021) was performed in a rice-broad bean-rice-garlic rotation system using four treatments: CK, without fertilizer; CF, chemical fertilizer only; T40, 40 % of chemical nitrogen replaced by organic fertilizer; T100, 100 % of chemical nitrogen replaced by organic fertilizer. The results showed that long-term use of T40 not only increased the levels of soil nutrients (carbon and nitrogen) and stabilized the pH but also had a positive effect on garlic yield compared with CF. Appling organic fertilizers increased the diversity of bacteria but reduced fungal diversity, which may be related to the rotation pattern. Organic fertilizers (T40, T100) also increased the relative abundance of beneficial microbes, which promoted nutrient cycling and plant growth. However, the application of chemical fertilizers alone (CF) or large amounts of organic fertilizer (T100) for extended times promoted the growth of methanogens, which might lead to increased CH4 emissions. The potentially favorable microbes (Pseudaleuria, Mortierella, and Lophotrichus) were positively associated with garlic yield, shown by Spearman's correlation analysis. Organic fertilizer enhanced the complexity of the soil bacterial and archaeal co-occurrences/interactions and stimulated competitive relationships between bacteria, as shown by network analysis. However, the fungal network showed the opposite trend, which may be related to the fact that organic fertilizers could provide more favorable growth conditions for saprophytic fungi. In summary, organic fertilizer used as a partial replacement for chemical fertilizer increased soil nutrient content and altered both the diversity and functions of soil microbial communities, thereby improving garlic productivity. It could be concluded that 40 % of the total nitrogen from organic fertilizers and the remaining 60 % from chemical fertilizers was a reasonable fertilization scheme for garlic in rice-broad bean-rice-garlic rotation system.