Mechanisms of nickel sorption by a bacteriogenic birnessite

A synergistic experimental-computational approach was used to study the molecular-scale mechanisms of Ni sorption at varying loadings and at pH 6-8 on the biogenic hexagonal birnessite produced by Pseudomonas putida GB-1. We found that Ni is scavenged effectively by bacterial biomass-birnessite assemblages. At surface excess values below 0.18 mol Ni kg⁻¹ sorbent (0.13 mol Ni mol⁻¹ Mn), the biomass component of the sorbent did not interfere with Ni sorption on mineral sites. Extended X-ray absorption fine structure (EXAFS) spectra showed two dominant coordination environments: Ni bound as a triple-corner-sharing (Ni-TCS) complex at vacancy sites and Ni incorporated (Ni-inc) into the MnO₂ sheet, with the latter form of Ni favored at high sorptive concentrations and decreased proton activity. In parallel to our spectral analysis, first-principles geometry optimizations based on density functional theory (DFT) were performed to investigate the structure of Ni surface complexes at vacancy sites. Excellent agreement was achieved between EXAFS- and DFT-derived structural parameters for Ni-TCS and Ni-inc. Reaction-path calculations revealed a pH-dependent energy barrier associated with the transition from Ni-TCS to Ni-inc. Our results are consistent with the rate-limited incorporation of Ni at vacancy sites in our sorption samples, but near-equilibrium state of Ni in birnessite phases found in nodule samples. This study thus provides direct and quantitative evidence of the factors governing the occurrence of Ni adsorption versus Ni incorporation in biogenic hexagonal birnessite, a key mineral in the terrestrial manganese cycle.