Soil productivity largely depends on the microorganisms present in the soil. Soil bacterial diversity is closely related to many biochemical processes occurring in the soil, and thus is important for plant growth (de Vries et al. 2020). A lot of attention has been focused on the role of microbial diversity on agriculture production. Although it is generally accepted it was necessary to maintain high biodiversity for sustainable agricultural production, the relationship between biodiversity and agricultural production has rarely been quantified, and there were still arguments that whether plants always benefited from the diverse microbial community. Our results indicated that the relationship between microbial diversity and crop production was significantly affected by anthropogenic activities. Although all treatments could significantly improve crop production (yield), they had different effects on soil bacterial diversity. IC and OF not only increased soil bacterial diversity, but also promoted crop yield. The CF treatment showed the highest efficiency in improving crop productivity, compared to other agricultural strategies (Fig. 1b), however, it had no positive effects on soil bacterial diversity, suggesting it might not be a sustainable strategy for agriculture production. To pursue high crop production, chemical fertilizers were often used, as they provide direct nutrients to crops, however, the disadvantages of chemical fertilizer application were widely reported. For instance, Long-term chemical fertilizing could lead to environmental risks and soil degradation (Zhou et al. 2015), particularly, it enriched microbes with certain functions that had strong competition ability, and therefore, led to community basis. This could explain why CF had negative effects on soil bacterial diversity.
To alleviate the negative effects caused by chemical fertilizers, organic matter fertilizers, green manure, plant rotation, or other approaches were often used (Lin et al. 2019; Zhang et al. 2020). Other than providing the soil with a lot of nutrients, organic fertilizers also improved soil microbial diversity. Although compared to chemical fertilizers, organic fertilizers had relatively weak effects in improving crop yield, they were considered to be a sustainable substance (Li et al. 2017; van der Bom et al. 2018), as they can improve soil fertility, increase soil bacterial community diversity and beneficial bacteria. It is generally accepted that organic fertilizers affected soil microbial biomass and bacterial community diversity by transporting organic matter to soil (Cookson et al. 2008) and the changes in bacterial community diversity would affect soil nutrient supply, thus indirectly affecting the yield (Chen et al. 2017; Mikanova et al. 2009).
IC increased both soil bacterial diversity and crop yield. In addition, soil bacterial diversity showed to have a positive relationship with crop yield under this treatment (p < 0.01, Fig. 2a, b). The species and types of plants can affect the structure of the soil microbial community through root exudates, intercropping or crop rotation mediated soil microbe pes (Brooker et al. 2015; Chadfield et al. 2022). Intercropping and rotation affect the composition and diversity of soil bacterial community through the exudates of different plant roots (Bais et al. 2006; Ladygina and Hedlund 2010), resulting in increased soil microbial diversity and crop yield (Stefan et al. 2021). The increase in crop productivity was related to the changing soil microbial community, especially the changes in the bacterial community, which is beneficial to plant growth. Increased diversity in soil bacterial communities can enrich beneficial bacteria, reduce pathogens that cause crop diseases, and facilitate microbial activity and the transport and absorption of nutrients needed by plants, thereby increasing crop yields (Alvey et al. 2003; Hauggaard-Nielsen and Jensen 2005; Li et al. 2014; Warembourg et al. 2003).
Microbial inoculation can provide soil with high-density microorganisms, causing at least temporary changes in the structure of the soil microbial community (Xi et al. 2015). However, our results showed that MF had no significant effect on soil bacterial community diversity in general, but it was also a measure that could improve crop yield (Fig. 1). Microbial inoculation may only have a significant impact on the diversity of some specific bacterial communities or some rare communities, so the results have no significant impact on the diversity of the entire soil bacterial community (Mawarda et al. 2020). Microbial inoculation can inoculate beneficial bacteria, resist pathogenic bacteria, protect plant health (Arora and Mishra 2017), or affect soil microbial diversity, thus affecting nutrient cycling, promoting plant absorption of nutrients, and indirectly increasing yield (Nassal et al. 2018).
Our results showed that higher soil microbial diversity did not always lead to higher plant productivity. Experimental scales, plant type, soil range, and pH value all affect the effects of agricultural management on soil bacterial diversity and crop yield, and the relationship between them (Fig. 2, S1-S5).
Intercropping and rotation can directly affect the composition and rhizosphere soil bacterial diversity through root exudates, thus improving soil fertility, promoting nutrient cycling and increasing crop yield (Gong et al. 2019; Zhalnina et al. 2018). The rhizosphere is the area that has been mostly affected by root exudates, whereas the bulk soil was seldom affected (Fan et al. 2018; Ling et al. 2022). Thus it was not suprising to find bacterial diversity in the rhizosphere and bulk soil responded differently to IC treatment (Fig. 1a). Changes in the rhizosphere microbial community can affect bulk microbiota (Kent and Triplett 2002), the rhizosphere is the main place where soil microorganisms participate in nutrient cycling and metabolite output (Bulgarelli et al. 2013). Therefore, intercropping and rotation could also promote crop production by mediating rhizosphere microbial diversity (Fig. 2a, d and S2). The use of organic fertilizers is helpful to improve the diversity of bacteria community in both bulk and rhizosphere soil (Fig. 2a). Organic fertilizer can provide the soil with organic matter, reduce soil bulk density, improve microbial activity and diversity throughout the soil, and speed up the process of nutrient cycling (Qaswar et al. 2020; Samuel et al. 2018). Therefore, it has the same influence trend on the bulk and rhizosphere soil bacterial community and improves yield (Fig. 1a, b). It should be noted that although CF had no significant effect on the rhizosphere and bulk bacterial diversity, there was a significant negative correlation between the rhizosphere bacterial diversity and crop yield under CF treatment in regression analysis (p < 0.01, Fig. 2a, c). This may be because the application of chemical fertilizer mainly provides a large amount of nutrients for plant growth, but does not provide too much organic matter to soil. In this case, there is a negative feedback relationship between the two (Ho and Chambers 2019; in't Zandt et al. 2019; Petermann et al. 2008).
The effects of agricultural management approaches on soil bacterial diversity and yield will be affected by the experimental scales. In the field experiment, MF reduced soil bacterial diversity, but in the pot experiment, it was the opposite (Fig. 1a). Compared with field experiments, pot experiments were relatively small and closed systems, with roots able to explore the whole range (Aragao et al. 2020). In addition, in the field experiment, the soil microbial environment is relatively complex and easily affected by climate, temperature, precipitation and other external factors, which may be the reason for the inconsistent influence of the two experimental scales in the microbial inoculation experiment (Liu et al. 2017).
Our results also showed that C3 and C4 plant yields and soil bacterial diversity were affected differently by agricultural management approaches (Fig. 1a, b), this could be due to different metabolisms between C3 and C4 plants (Taylor et al. 2010). CF could increase the yield of C3 and C4 crops, but had different effects on the soil bacterial diversity (Fig. 1). The use of inorganic fertilizers, especially nitrogen fertilizers, will affect soil organic matter and carbon cycling (Rubio et al. 2010). C4 plants have higher photosynthetic efficiency than C3 plants (Zhu et al. 2008), and the composition and diversity of soil bacterial community affect C cycle and turnover (Ramirez et al. 2012; Zang et al. 2016), We speculated that the application of inorganic fertilizer affected the turnover of C, and C4 plants needed a higher diversity of soil bacterial community to participate in this process, resulting in the different effects of inorganic fertilizer on the diversity of soil bacterial community of C3 and C4 plants. pH has a great influence on the diversity and composition of the soil bacterial community (Zhou et al. 2015). Only in the pH range of 6–8, OF and MF had an effect on the soil bacterial diversity. Agricultural management approaches had no significant effect on soil bacterial diversity in overly acidic or overly alkaline soils (Fig. 1a). This may be because the range of pH values suitable for the growth of bacterial community is relatively small, and an overly acidic or alkaline environment is not conducive to the growth of soil bacterial community (Rousk et al. 2010).
Different agricultural management strategies should be adopted when pursuing different economic benefits and protecting ecological environments. Our study can provide some reference for improving crop yield and soil bacterial diversity, and has certain significance for ecological environment protection and improving crop economy. In the short term, if environmental concerns are not considered and crop yields are pursued, our analysis suggests that chemical fertilizer is a better choice. However, if you want to sustain crop yield while also improving soil fertility, microbial diversity, and the soil environment, you can use organic fertilizer. Although organic fertilizers do not significantly improve crop yields as chemical fertilizers do, they are a sustainable agricultural management strategy that improves soil fertility, microbial activity and diversity, as well as crop yields (Gravuer et al. 2019; Li et al. 2021; Young et al. 2021). Intercropping and crop rotation are also good choices, there are also many studies that combine the advantages of these agricultural management approaches, such as the combined use of organic and inorganic fertilizers or crop rotation and organic fertilizers, to maximize yield and improve soil microbial diversity (Ghaley et al. 2005; Li et al. 2022; Mei et al. 2021; Salehi et al. 2017).