Genomic and Functional Characterization of the Calcite-Precipitating Bacterium Bacillus paralicheniformis ITBMC36: A Promising Agent for Self-Healing Concrete

Cracking is a major cause of concrete deterioration because it allows water and aggressive ions to penetrate the material and accelerate structural damage. Microbially induced calcite precipitation (MICP) has emerged as a promising strategy for crack repair because selected bacteria can precipitate calcium carbonate and thereby seal damaged regions. In this study, we characterized strain ITBMC36, a calcite-precipitating bacterium isolated from a limestone-rich environment in Vietnam, and evaluated its potential for MICP-based crack repair. Strain ITBMC36 produced 26.73 ± 0.81 g/L of mineral precipitate in B4 medium. Mineral characterization showed that the precipitate consisted mainly of calcite, with minor amounts of vaterite and aragonite. Enzymatic assays showed urease activity of 35.71 ± 1.24 U/mL and carbonic anhydrase activity of 1.627 ± 0.010 U/mL. Hybrid genome sequencing generated a complete circular chromosome of 4,410,549 bp, and genome-based taxonomic analysis identified the isolate as Bacillus paralicheniformis. Genome mining revealed traits relevant to MICP and survival in cementitious environments, including a complete urea uptake and urease system, five putative carbonic anhydrase genes, exopolysaccharide and biofilm-associated loci, and multiple genes involved in stress response, pH homeostasis, and sporulation. In mortar specimens containing artificial microcracks (0.5 ± 0.1 mm), ITBMC36 promoted progressive crack closure, with visible mineral deposition by day 7 and near-complete sealing by day 35. Together, these results identify B. paralicheniformis ITBMC36 as a promising, locally sourced bacterium for MICP-based crack repair and provide a high-quality genome resource for future optimization of bio-based cementitious materials.