Since, the LD slag is rich in fertilizer components, its application remarkably increased nutrients (mostly C, P, Si, Fe, and Mg) in soil, consequently nutrients (N, P, and Si) acquisition by the plant and the crop yield. A favorable soil pH (towards neutral) under the slag amendment might enhance nutrient mineralization11. Silicon-induced higher plant photosynthesis and probably the resistance of rice plants to biotic and abiotic stress1,5 could be another reason for higher crop yield under the slag amendment. Increased shoot biomass likely increased plant N acquisition, which in turn decreased soil N availability in slag amendment treatments.

The increased activities of most of the soil enzymes having a role in carbon, nitrogen, and phosporous cycling indicated increased soil nutrient turnover under the slag amendment. The increased activities of soil enzymes could be explained by increased substrate availability and microbial biomass in response to the slag amendment25. The more labile carbon availability through Si-induced root exudation5,13 might have induced an increase in labile carbon degrading enzymes compared to recalcitrant carbon degrading enzymes.

This study evidenced that the rhizosphere bacterial communities were more rich and less even under the slag amendment, irrespective of rice cultivars (Table 2). The nutrient availability under the slag amendment might enhance r-strategic bacteria, resulting in more uneven bacterial communities that flourish more adequately under the increased availability of accessible nutrients26. However, this result should not be extrapolated to generalize that bacterial community under the slag amendment is consistently richer and less even over the whole cropping season, because in this study, bacterial community and diversity were estimated after harvesting. Moreover, since, rare species can also strongly influence ecosystem functioning, it is difficult to interpret the shift in richness and evenness with respect to crop management practices27. Hence, we focus our discussion on the shift in bacterial communities and the significantly influenced bacterial taxa which play a beneficial or detrimental role in the agro-ecosystem.

Proteobacteria were the most dominant phyla which significantly increased in slag amendment treatments compared with unamended treatments, irrespective of rice cultivars. The increase in relative abundance of Proteobacteria is likely due to the copiotrophic nature of the phyla which has been shown to proliferate under greater carbon availability26. Within Proteobacteria, Betaproteobacteria and Alphaproteobacteria were significantly increased in the slag amendment treatments. It has been postulated that Betaproteobacteria respond promptly to carbon availability, and are among the dominant inhabitants of paddy rhizosphere28,29. The members of the class Alphaproteobacteria are commonly known for their sole role in N 2 -fixation30 and their increase indicates that the LD slag amendment can be considered to stimulate N 2 -fixing ability of paddy soil. The higher photosynthesis and shoot biomass could enhance plant N uptake and thus decline available N in soil, in slag amendment treatments. The N deficiency is supposed to stimulate N 2 -fixing microorganisms in soil amended with the slag. Next to Proteobacteria, the phylum Actinobacteria significantly increased under the slag amendment. Actinobacteria play an important role in organic matter decomposition and biological buffering of soils31,32. Their relative increase probably facilitates nutrient mobilization in slag amended soils. However, discrepancy exists with regards to the occurrence of Actinobacteria in C-limited and -enriched ecosystems17,19. Unlike Proteobacteria and Actinobacteria, Acidobacteria, Bacteroidetes, Nitrospirae, and Chloroflexi were significantly decreased due to the slag fertilizer application. The decrease in relative abundance of Acidobacteria is likely due to the oligotrophic nature of the phylum and a strong negative correlation with soil pH26. Becteroidetes are in general considered to have an important role in the degradation of complex organic matter, especially polysachharides33. The higher labile carbon availability through increased root exudation under the slag amendment could diminish the role of Bacteroidetes to degrade complex organic matter. The low relative abundance of Nitrospirae, and Chloroflexi may be due to their adaptation to nitrogen limitation and flexibility for the limiting nutrient under slag amendment conditions34. In contrast to our findings, Bacteroidetes and Chloroflexi have been found to dominate in C-rich and N-rich environments, respectively15,18. Consequently, whereas there is a consensus that agronomic management practices alters soil microbial communities, the response of individual groups appears to be very context-specific and cannot be generalized across various agro-ecosystems27. The response is mostly dependent on soil physicochemical changes induced by the agronomic practices, which again differ among different soil types and under different climatic conditions.

Structural redundancy is widespread at higher taxonomic level. Taxonomy compositions at the lower (genus and species) level can differ significantly35. In this study, genera Geobacter and Pelobacter and species Geobacter pickeringii, Thermovenabulum ferriorganovorum, and Magnetospirillum magnetotacticum which are well known as Fe-reducer remarkably increased in response to the slag amendment (Table S3). Their increase might be due to greater Fe availability in slag amendment treatments. The increase in Fe-reducing bacteria under the slag amendment indicates that these bacteria could have a role in alleviating Fe-toxicity in the slag amended paddies. Species such as Clostridium caenicola, Clostridium termitidis, and Caldilinea tarbellica which are reported to have a role in carbohydrate utilization noticeably increased under the slag amendment, indicating that the slag amendment could stimulate C-degrading bacteria (Table S3). Likely, members of some dominant genera such as Bacillus, Azospirillum, and Clostridium and species such as Bacillus arbutinivorans, Bacillus aryabhattai, Bacillus pumilus, Bacillus niacin, and Azospirillum zeae, which have an important role in plant growth promoting (PGP) activities (Phytohormone production, P solubilization and N 2 -fixation) significantly increased under slag amendment treatments, indicating that the LD slag amendment in rice paddies could be promising to enhance PGP activities and hence crop yield.

A greater understanding of the regulatory factors (drivers) shaping rhizosphere microbiome is essential to use microbial technology for sustainable agriculture19. In agreement with our first hypothesis of this study, the slag amendment significantly increased nutrient availability in soil and consequently nutrient acquisition by the plant. These changes altered rhizosphere bacterial community composition, stimulated certain microbial taxa and induced soil enzyme activities. The soil nutrient availability and plant nutrient acquisition accounted for 39.7% and 13.3% of rhizosphere bacterial community variations (Fig. 4). In addition to soil nutrient fluxes, plant nutrient acquisition has been reported to alter soil microbial community composition16,19. According to our second hypothesis, the slag amendment remarkably increased Si concentrations in soil pore-water and likely enhanced photosynthesis and plant biomass. A significant contribution (15.6%) of plant attributes (photosynthesis and above and below ground biomass) to the variation in the rhizosphere bacterial community was observed. The rhizodeposition of organic C by the plant likely stimulated copiotrophic bacterial communities. Moreover, activities of certain oligotrophs could be stimulated by rhizodepoited-carbon, that further causes short term changes in SOM turnover by mineralizing the recalcitrant SOM, using fresh organic C as a source of energy14. In line with our third hypothesis, a significant contribution of soil pH to the variation in the rhizosphere bacterial community was observed. An increase in soil pH towards neutral value due to the slag amendment likely improved nutrient mobilization and thus microbial activities. Soil pH was identified as an important factor structuring microbial communities of agroecosystems36. Noteworthy, large differences in nutrient uptake between Indica and Japonica rice species, even without the slag amendment were observed. Rice species or cultivar variation has been reported to alter rhizosphere microbial community composition and nutrient cycling37,38. Plant species with high growth rate have higher rates of root exudation and labile compounds that can fuel rhizosphere microbial community37,38. The mantel test analysis revealed that RMC, MBC, aqSi, aqFe, straw and root biomass, and N, P, and Si uptake (straw only) significantly correlated with rhizosphere bacterial communities in control (without slag) treatments (Table 4).

In conclusion, the short-term LD slag amendment in rice cropping systems enhanced microbial biomass and activities, which increased nutrient availability in soil and nutrient uptake by the plant, finally improving crop yield. Our recent study also witnessed no heavy metal contamination in rice grain in response to short-term LD slag amendment11. The application of slag in the long term may increase soil alkalinity and accumulate heavy metals in soils, which may hinder soil microbial communities and functions and thus the crop yield. Long-term studies in different soil and environmental conditions are essential to clearly know the changes in soil microbial communities, their functional roles, and the crop yield under slag-based soil amendments in agriculture.