Genomic and Transcriptomic Insights into Calcium Carbonate Biomineralization by Marine Actinobacterium Brevibacterium linens BS258

Abstract

Calcium carbonate (CaCO₃) biomineralization has been investigated due to its wide range of scientific and technological implications, however, the molecular mechanisms of this important geomicrobiological process are largely unknown. Here, a urease-positive marine actinobacterium <i>Brevibacterium linens</i> BS258 was demonstrated to effectively form CaCO₃ precipitates. Surprisingly, this bacterium could also dissolve the formed CaCO₃ with the increase of the Ca²⁺ concentration. To disclose the mechanisms of biomineralization, the genome of <i>B. linens</i> BS258 was further completely sequenced. Interestingly, the expression of three carbonic anhydrases was significantly up-regulated along with the increase of Ca²⁺ concentration and the extent of calcite dissolution. Moreover, transcriptome analyses revealed that increasing concentration of Ca²⁺ induced KEGG pathways including quorum sensing (QS) in <i>B. linens</i> BS258. Notably, most up-regulated genes related to QS were found to encode peptide/nickel ABC transporters, which suggested that nickel uptake and its associated urease stimulation were essential to boost CaCO₃ biomineralization. Within the genome of <i>B. linens</i> BS258, there are both cadmium and lead resistance gene clusters. Therefore, the sequestration abilities of Cd²⁺ and Pb²⁺ by <i>B. linens</i> BS258 were checked. Consistently, Pb²⁺ and Cd²⁺ could be effectively sequestered with the precipitation of calcite by <i>B. linens</i> BS258. To our knowledge, this is the first study investigating the microbial CaCO₃ biomineralization from both genomic and transcriptomic insights, which paves the way to disclose the relationships among bacterial metabolisms and the biomineralization.