1
|
Sorokina LV, Phakatkar AH, Rehak PL, Král P, Shokuhfar T, Shahbazian-Yassar R. Nickel as a modifier of calcium oxalate: an in situ liquid cell TEM investigation of nucleation and growth. Nanoscale 2024; 16:4266-4274. [PMID: 38348770 DOI: 10.1039/d3nr05314h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Despite extensive research on the nucleation and growth of calcium oxalate (CaOx) crystals, there are still several challenges and unknowns that remain. In particular, the role of trace metal elements in the promotion or inhibition of CaOx crystals is not well understood. In the present study, in situ graphene liquid cell transmission electron microscopy (in situ GLC TEM) was used to observe real-time, nanoscale transformations of CaOx crystals in the presence of nickel ions (Ni2+). The results showed that Ni2+ form Ni-water complexes, acting as a shape-directing species, generating a unique morphology and altering growth kinetics. Transient adsorption of Ni-water complexes resulted in a metastable phase formation of calcium oxalate trihydrate. Atomistic molecular dynamics simulations confirmed that Ni2+ acts as a weak inhibitor which slows down the CaOx crystallization, elucidating that Ni2+ impacts small-sized CaOx clusters by bringing more water into the clusters. This work highlighted the intricacies behind the effect of Ni2+ on CaOx biomineralization that were made possible to discern using in situ GLC TEM.
Collapse
Affiliation(s)
- Lioudmila V Sorokina
- Department of Civil, Materials, and Environmental Engineering, University of Illinois Chicago, Chicago, IL, 60607, USA.
| | - Abhijit H Phakatkar
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Pavel L Rehak
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Petr Král
- Departments of Chemistry, Physics, Pharmaceutical Sciences, and Chemical Engineering, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Tolou Shokuhfar
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL, 60607, USA
- Department of Mechanical and Industrial Engineering, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Reza Shahbazian-Yassar
- Department of Civil, Materials, and Environmental Engineering, University of Illinois Chicago, Chicago, IL, 60607, USA.
- Department of Mechanical and Industrial Engineering, University of Illinois Chicago, Chicago, IL, 60607, USA
| |
Collapse
|
2
|
Sonke A, Trembath-Reichert E. Expanding the taxonomic and environmental extent of an underexplored carbon metabolism-oxalotrophy. Front Microbiol 2023; 14:1161937. [PMID: 37213515 PMCID: PMC10192776 DOI: 10.3389/fmicb.2023.1161937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/11/2023] [Indexed: 05/23/2023] Open
Abstract
Oxalate serves various functions in the biological processes of plants, fungi, bacteria, and animals. It occurs naturally in the minerals weddellite and whewellite (calcium oxalates) or as oxalic acid. The environmental accumulation of oxalate is disproportionately low compared to the prevalence of highly productive oxalogens, namely plants. It is hypothesized that oxalotrophic microbes limit oxalate accumulation by degrading oxalate minerals to carbonates via an under-explored biogeochemical cycle known as the oxalate-carbonate pathway (OCP). Neither the diversity nor the ecology of oxalotrophic bacteria is fully understood. This research investigated the phylogenetic relationships of the bacterial genes oxc, frc, oxdC, and oxlT, which encode key enzymes for oxalotrophy, using bioinformatic approaches and publicly available omics datasets. Phylogenetic trees of oxc and oxdC genes demonstrated grouping by both source environment and taxonomy. All four trees included genes from metagenome-assembled genomes (MAGs) that contained novel lineages and environments for oxalotrophs. In particular, sequences of each gene were recovered from marine environments. These results were supported with marine transcriptome sequences and description of key amino acid residue conservation. Additionally, we investigated the theoretical energy yield from oxalotrophy across marine-relevant pressure and temperature conditions and found similar standard state Gibbs free energy to "low energy" marine sediment metabolisms, such as anaerobic oxidation of methane coupled to sulfate reduction. These findings suggest further need to understand the role of bacterial oxalotrophy in the OCP, particularly in marine environments, and its contribution to global carbon cycling.
Collapse
|