Characterization and genome analysis of Neobacillus mesonae NS-6, a ureolysis-driven strain inducing calcium carbonate precipitation

Rui Xu; Shuqi Zhang; Zhiwei Ma; Qingyan Rao; Yanling Ma

doi:10.3389/fmicb.2023.1277709

Characterization and genome analysis of Neobacillus mesonae NS-6, a ureolysis-driven strain inducing calcium carbonate precipitation

Front Microbiol. 2023 Nov 1:14:1277709. doi: 10.3389/fmicb.2023.1277709. eCollection 2023.

Authors

Rui Xu¹, Shuqi Zhang¹, Zhiwei Ma¹, Qingyan Rao¹, Yanling Ma²

Affiliations

¹ College of Life Science, Northwest University, Xi'an, Shaanxi, China.
² Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, Shaanxi, China.

Abstract

In this study, a highly promising bacterium was isolated from sandstone oil in the Ordos Basin, named strain NS-6 which exhibited exceptional urease production ability and demonstrated superior efficiency in inducing the deposition of calcium carbonate (CaCO₃). Through morphological and physiochemical characteristics analysis, as well as 16S rRNA sequencing, strain NS-6 was identified as Neobacillus mesonae. The activity of urease and the formation of CaCO₃ increased over time, reaching a maximum of 7.9 mmol/L/min and 184 mg (4.60 mg/mL) respectively at 32 h of incubation. Scanning Electron Microscopy (SEM) revealed CaCO₃ crystals ranging in size from 5 to 6 μm, and Energy Dispersive X-ray (EDX) analysis verified the presence of calcium, carbon, and oxygen within the crystals. X-ray Diffraction (XRD) analysis further confirmed the composition of these CaCO₃ crystals as calcite and vaterite. Furthermore, the maximum deposition of CaCO₃ by strain NS-6 was achieved using response surface methodology (RSM), amounting to 193.8 mg (4.845 mg/mL) when the concentration of calcium ions was 0.5 mmol/L supplemented with 0.9 mmol/L of urea at pH 8.0. Genome-wide analysis revealed that strain NS-6 possesses a chromosome of 5,736,360 base pairs, containing 5,442 predicted genes, including 3,966 predicted functional genes and 1,476 functionally unknown genes. Genes like ureA, ureB, and ureC related to urea catabolism were identified by gene annotation, indicating that strain NS-6 is a typical urease-producing bacterium and possesses a serial of genes involved in metabolic pathways that mediated the deposition of CaCO₃ at genetic level.

Keywords: Neobacillus mesonae; biomineralization; calcium carbonate; response surface methodology; urease activity; whole-genome sequencing.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The authors would like to acknowledge the support received from the National Natural Science Foundation of China (grant number 31000069) and the Key Project on Social Development of Science and Technology in Shaanxi Province (grant number 2017ZDXM-SF-105).