Lysinibacillus irui strain:AFB02
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ABSTRACT:
PROVIDER: PRJNA1321292 | ENA |
REPOSITORIES: ENA
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Project description:Microbially induced calcium carbonate precipitation (MICP) holds potential for soil stabilization and carbon sequestration efforts. While the biogeochemical pathways and enzymes driving MICP are known, the microbial metabolic networks and community dynamics underlying such processes remain poorly characterized. To address this gap, we interrogated a MICP-capable four-member consortium of soil bacteria termed carbon storing consortium - A (CSC-A). Prior work shows that CSC-A yields carbonate at a higher quantity compared to the sum of carbonate individually produced by each member, suggesting MICP is driven by consortium dynamics.Thus, we applied a multi-omic integration approach of genomics, transcriptomics, and metabolomics to investigate potential inter-species interactions that may influence the MICP phenotype. Genomic life history characterizations identified evidence of specialization by two members, while metatranscriptomic perturbation suggested that R. qingshengii is a keystone species when grown in urea, a key molecule to the MICP process. By comparing individual species’ metabolomes to the metabolic profile of a shared well, we identified over 200 metabolites predicted to be produced or consumed by CSC-A. Integrating both data types and mapping them to the KEGG reactome highlighted over 20 different enriched pathways with reactions related to glutamate metabolism, succinate metabolism, and branched chain amino acid biosynthesis. As succinate metabolism was a major node in this network we applied laboratory assays to confirm that succinate led to increased carbonate precipitation by CSC-A, a critical validation of our modeling approach. By isolating and identifying the interconnected metabolic components underlying MICP in CSC-A, we identified keystone taxa, metabolites, and pathways important for future optimization of the application of this consortium to carbonate precipitation.
2026-02-26 | GSE320329 | GEO
Project description:Microbially induced carbonate precipitation (MICP) refers to the biogeochemical process in which calcium carbonate is precipitated by altering the local geochemical environment (Mortensen et al. 2011). These alterations occur as a by-product of common microbial metabolic activities by increasing the local carbonate content as well as pH thereby saturating the solution in respect to carbonate. To better understand the microbial ecology of MICP on a community level in natural environments, we chose to evaluate microbial communities derived from travertine adjacent to Crystal Geyser (CG), Utah. CG is a cold-driven, CO2 rich geyser which is surrounded by colorful travertine that has been suggested to be generated through microbial processes. We used a cultivation-independent, multi-omics approach combined with geochemical measurements to investigate metabolic pathways and physiologies potentially involved in MICP at CG. We collected samples from the top 20 cm of travertine adjacent to Crystal Geyser, Utah in November 2019 and June 2021 (38.9384° N, 110.1354° W) wearing gloves at all times. We sampled 1 m away from the borehole (CG-1) and 10 m away from the borehole (CG-10). We preserved all collected samples in RNAlater-like solution (Menke et al., 2017, Front. Microbiol. 8) in a 1:10 sediment: RNAlater-like solution ratio as previously validated (Jensen et al. (2021, Micro. Spec. 2021, 9:2)
2024-11-18 | PXD041379 | Pride
Project description:We developed a microbial catalytic concept and strategy to prepare calcium carbonate with micro/nanostructures on the surface of bioceramics to improve bone-forming bioactivity. It involves three processes: bacterial adhesion on biomaterials, production of carbonate assisted with bacteria, nucleation and growth of calcium carbonate nano-crystals on the surface of bioceramics. The microbially catalyzed biominerals exhibited relatively uniform micro/nanostructures on both 2D and 3D CaSiO3 bioceramics. The descriptive analysis of RNA-sequencing revealed that the topographic and chemical cues presented by microbially catalyzed micro/nanostructures could stimulate the biological processes including adhesion, proliferation and differentiation. The study offers a microbially catalytic concept and strategy of fabricating micro/nanostructured biomaterials for tissue regeneration.
2020-11-26 | GSE162127 | GEO
Project description:Bacteria isolated from the cement capable of forming calcium carbonate crystals
| PRJEB32639 | ENA
Project description:Amorphous calcium carbonate (ACC) is a non-crystalline form of calcium carbonate, which is composed of aggregated nano-size primary particles. Here, we wanted to evaluate how ACC affects gene expression in a human lung cancer cell line (A549).
2023-08-21 | GSE235316 | GEO
Project description:Lysinibacillus irui strain:B3 Genome sequencing and assembly
| PRJNA1050580 | ENA
Project description:Lysinibacillus irui strain:B2 Genome sequencing and assembly
| PRJNA1049478 | ENA