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Liming materials have been extensively used to immobilize heavy metals. Bacteria, archaea, and fungi are sensitive to heavy metals and play critical roles in soil biogeochemical cycling and crop health. However, the responses of bacteria, archaea, and fungi to liming materials in agricultural soils contaminated with heavy metals are still unclear. A field experiment was conducted to assess the effect of liming on the three microbial domains and the potential influencing factors in maize-planted agricultural soil contaminated with Cd and Pb. Using a high-throughput sequencing method, we found that liming materials enhanced copiotrophic bacteria (Proteobacteria, Gemmatimonadetes, and Bacteroidetes), Bathyarchaeota, and arbuscular fungi (Glomeromycota) but suppressed some oligotrophic bacteria (Chloroflexi) and saprotrophic fungi. Notably, soil-available Cd markedly influenced the community composition of prokaryotes but not that of eukaryotes. Similar edaphic factors were correlated with the relative abundance of dominant bacterial and archaeal taxa but with opposite effects. Furthermore, co-occurrence network analysis revealed that the complexity decreased but the fungal nodes and edges increased after liming, indicating that the microbial community was not highly resilient to environmental stresses and the importance of fungi in community structure was enhanced. Overall, these findings suggest that changes in microorganisms resulting from liming facilitate soil biogeochemical cycles but suppress microbial stability, potentially affecting the sustainable use of agricultural soils contaminated with heavy metals. • Liming material was applied to an agricultural soil with Cd and Pb contamination. • Liming enhanced copiotrophic but suppressed oligotrophic microbes. • Liming affected microbial communities by different mechanisms. • Microbial network complexity decreased but the importance of fungi increased. [ABSTRACT FROM AUTHOR]

Liming is widely used to ameliorate acidic soils. However, few studies have addressed the effects of different lime application rates on soil microbial communities. Specifically, the effects of liming on fungal communities remain largely unknown. Here, we set up a gradient of increasing lime application rates, 0, 450, 900, 1350, 1800, 2250, 3000, and 3750 kg ha−1, to investigate the effects of lime inputs on soil properties and community diversity and composition of prokaryotes and fungi in paddy soils. Our results showed that the effect of liming on soil pH improvement become insignificant when the application rate exceeded 1800 kg ha−1. Prokaryotic diversity and community composition were both significantly influenced by liming, whereas fungal communities were less responsive. Nonetheless, the promotive effects of liming on soil prokaryotic diversity declined when lime application rates exceeded 900 kg ha−1 (or pH > 6.5). Soil pH was the key factor shaping the prokaryotic community, while pH and SOM were both important in explaining the observed variation in fungal communities. Distinct responses of ammonia oxidizing archaea (AOA) lineages were also observed as pH increased. Our results provide insights into the complex responses of both prokaryotic and fungal communities to lime application in paddy soils, and suggest that the amount of lime applied is also important for maintaining a healthy and sustainable soil environment. • Prokaryotes were more responsive to liming than fungi. • Liming effects on prokaryotes vanished when application rates exceeded 900 kg ha−1. • AOA lineages showed distinct responses to increasing lime inputs. • pH was the key factor shaping the prokaryotic community. • Fungal community diversity and composition were linked to both pH and SOM. [ABSTRACT FROM AUTHOR]