Long-term intensive use of mineral fertilizers in double rice-cropping systems has led to soil acidification and soil degradation. Manure fertilization was suggested as an alternative strategy to mitigate soil degradation. However, the effects of long-term mineral and manure fertilization on rice grain yield, yield stability, soil organic carbon (SOC) content, soil total nitrogen (TN) content, and the underlying mechanisms are unclear. Based on a long-term experiment established in 1981 in southern China, we compared four treatments: no fertilizer application (Control); application of nitrogen–phosphorus–potassium (NPK); NPK plus green manure in early rice (M1); and M1 plus farmyard manure in late rice and rice straw return in winter (M2). Our results showed that 37 years of NPK, M1, and M2 significantly increased rice grain yield by 54%, 46%, and 72%, and yield stability by 22%, 17%, and 9%, respectively. M1 and M2 significantly increased SOC content by 39% and 23% compared to Control, respectively, whereas there was no difference between Control and NPK. Regarding soil TN content, it was significantly increased by 8%, 46%, and 20% by NPK, M1, and M2, respectively. In addition, M2 significantly increased bacterial OTU richness by 68%, Chao1 index by 79%, and altered the bacterial community composition. Changes in soil nutrient availability and bacterial Simpson index were positively correlated with the changes in grain yield, while shifts in bacterial community were closely related to yield stability. This study provides pioneer comprehensive assessments of the simultaneous responses of grain yield, yield stability, SOC and TN content, nutrient availability, and bacterial community composition to long-term mineral and manure fertilization in a double rice-cropping system. Altogether, this study spanning nearly four decades provides new perspectives for developing sustainable yet intensive rice cultivation to meet growing global demands.

The storage of soil organic carbon (SOC) in cropland soils is an essential strategy that serves the dual purpose of enhancing soil fertility and mitigating climate change. However, how the stability of stored carbon is altered under long-term fertilization has not been well understood, especially in the double rice cropping system in Chinese paddy soils. In this study, we explored the SOC storage and consequent stability of SOC under long-term fertilization. The soil samples were fractionated chemically to isolate various fractions and constituent pools of SOC (i.e., very labile C/VLC, labile C/LC, less labile C/LLC, and non-labile C/NLC). The following treatments were tested: control (CK), recommended rate of inorganic fertilizer (NPK), double the amount of recommended rate of inorganic fertilizer (2NPK), and NPK combined with manure (NPKM). The results showed that, relative to the initial level, the application of NPKM significantly improved the SOC storage as compared to the control. The long-term NPKM increased the total SOC in the paddy soil and this increased SOC was mainly stored in LLC, as revealed by the highest increase (142%) over the control. Furthermore, the highest proportion of labile pool was associated with unfertilized CK, while the reverse was true for the recalcitrant pool, which was highest under NPKM. This supports the role of combining manure with NPK to improve the stability of SOC, further verified by the high recalcitrance index under NPKM (56.75% for 0–20 cm and 57.69% for 20–40 cm) as compared to the control.

Adequate exploitation of legume–rhizobia symbiosis for nitrogen fixation may help to alleviate the overuse of chemical nitrogen fertilizer and aid in sustainable agricultural development. However, controlling this beneficial interaction requires thorough characterization of the effects of soil rhizosphere microorganisms, especially core taxa, on the legume–rhizobia symbiosis. Here, we used Illumina sequencing to investigate the effects of cover crop (Raphanus sativus L. and Lolium perenne L.) residue on the rhizosphere soil microbial community and peanut nodulation ability. The results indicated that Raphanus sativus L. amendment (RS) significantly increased soil available phosphorus (AP) content and peanut nodulation ability, while the Lolium perenne L. amendment (LP) had no noticeable impact on peanut nodulation. LP and RS significantly elevated bacterial and rhizobial diversity, reduced fungal diversity, and shifted microbial community structure (bacteria, 14.7%, p = 0.001; rhizobia, 21.7%, p = 0.001; fungi, 25.5%, p = 0.001). Random forest analysis found that the core rhizosphere taxa, sharing similar ecological preferences, were the primary drivers of peanut nodulation. By least squares regression, soil AP content was found to be positively correlated with the relative abundance of key ecological clusters. Furthermore, RS was found to promote peanut nodulation by increasing the relative abundance of critical rhizosphere taxa. Overall, our findings emphasize that core microbial taxa might play an essential function in the modulation of legume nodulation and provide scientific evidence for the effective management of the plant microbiome.