The tea plant is an economically important crop in China, but long-term monoculture and substantial chemical nitrogen fertilizer input cause soil acidification, which in turn affects the nutrient supply and tea quality. Intercropping has drawn more attention in tea gardens because this pattern is expected to improve soil fertility and tea quality and change the soil microbial community composition. However, the roles of some key microorganisms in rhizosphere soils have not been well characterized. Here, a “soybean in summer and smooth vetch in winter” strategy was used in a tea garden to investigate the effects of intercropped legumes on soil fertility, tea quality, and potential changes in beneficial bacteria such as Bacillus. Our data showed that when soybeans were turned into the soil, the intercropping system exhibited higher soil organic matter (SOM), total nitrogen (TN), tea quality indices, and expression of the Camellia sinensis glutamine synthetase gene (CsGS). Notably, intercropping significantly affected the bacterial communities, decreasing the relative abundance of Bacillus but increasing its absolute abundance. Bacillus amyloliquefaciens BM1 was isolated from intercropped soil and showed outstanding plant growth-promoting (PGP) properties when co-inoculated with rhizobia. In winter, intercropping with smooth vetch had a beneficial effect on soil properties and tea quality. Co-inoculation with strain BM1 and Rhizobium leguminosarum Vic5 on smooth vetch (Vicia villosa) produced huge improvements in SOM, TN, and tea leaf quality, which were accompanied by the highest level of amino acids and the lowest levels of polyphenols and caffeine (p < 0.05). Our findings demonstrate that intercropping with some legumes in the tea garden is a strategy that increases SOM, TN, and tea quality, and the optional use of some PGP Bacillus species produces an amplification effect.

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