Transcriptomic and metabolic insights into the mechanism of cadmium biomineralization by Klebsiella michiganensis NT-27

Microbially induced calcite precipitation (MICP) offers a promising strategy for the remediation of cadmium (Cd) contamination; however, the molecular mechanisms underlying Cd immobilization during this process remain unclear. This study aimed to uncover the biomineralization mechanisms of Klebsiella michiganensis NT-27, a Cd-resistant and ureolytic bacteria. To achieve this, we conducted integrated genomic, transcriptomic, and metabolomic analyses. Results showed that K. michiganensis NT-27 effectively removed 70.97 % of Cd^2 + from a 20 mg/L solution in 7 days. Genomic analysis identified Cd²⁺ resistance genes (czcD, 945 bp; zntA, 2205 bp) and the complete urease gene cluster (ureABCDEFG), with ureC being the longest (1704 bp). Transcriptomic analysis identified 25 upregulated and 22 downregulated genes during the MICP process, primarily related to transmembrane transport, the TCA cycle, and glutamate metabolism. Metabolomic profiling showed significant changes in ABC transporters, arginine biosynthesis, biosynthesis of cofactors, and nucleotide metabolism. SEM-EDS, TEM, FTIR, XRD, and XPS analyses confirmed that Cd²⁺ was immobilized via co-precipitation with CaCO₃, while 3D-EEM analysis further indicated that tyrosine- and tryptophan-containing extracellular polymeric substances contributed to Cd²⁺ immobilization. These findings provide a comprehensive understanding of the molecular mechanisms driving Cd immobilization during the MICP process, offering valuable insights for the development of effective bioremediation strategies.