Comparative study of the effects of different carbon substrates on acidification-driven mineral weathering by Pseudomonas

ABSTRACT While carbon sources released by plant roots and fungi are known to favor the enrichment of mineral weathering (MWe) bacteria, their impact on MWe activity remains poorly understood. The relationships among bacterial MWe ability, metabolism, and carbon source utilization, therefore, remain to be elucidated. In this context, a collection of plant growth-promoting Pseudomonas strains, including the newly described strain Pseudomonas spelaei PML3(3), was screened for its ability to weather minerals [i.e., Ca 3 (PO 4 ) 2 and biotite]. The impact of 10 carbon sources was assessed, together with the underlying genetic basis of these strains, by combining in vitro bioassays and geochemical and in silico analyses. The strains were ranked according to their MWe abilities in the different assays. All the strains were able to weather at least one mineral type, and their effectiveness depended on the substrate metabolized, with the strain PML3(3) generally being the most effective. Comparative genomic analyses linked the ability of the different strains to acidify the solution and produce organic acids, such as gluconate, to specific genomic organizations. Further analyses revealed that acidification-driven MWe was delayed when mannitol, rather than glucose, was used as the sole carbon source, suggesting that, depending on the substrate, either a single pathway, such as the direct oxidative glucose pathway, or multiple metabolic pathways may operate simultaneously to confer mineral weathering ability to bacteria. Our new findings demonstrate that MWe by bacteria strongly relies on carbon metabolism and represents a more dynamic and complex process than previously expected. IMPORTANCE In this work, we investigated the acidification-driven mineral weathering (MWe) mechanism and its genetic basis in a collection of Pseudomonas strains, including the model strain Pseudomonas spelaei PML3(3). Comparative genomic analyses revealed two major genomic organizations associated with the direct oxidative (DO) pathway of glucose that are commonly found within the genus Pseudomonas : (i) a system comprising only a pyrroloquinoline quinone (PQQ)-dependent glucose dehydrogenase (GDH) and (ii) a system comprising a PQQ-dependent GDH and a FAD-dependent gluconate dehydrogenase (GADH). These results indicate that the enzymes involved in the DO pathway of glucose are broadly conserved across the genus. Our results revealed intragenus variability in the MWe abilities of Pseudomonas strains isolated from diverse environments. In vitro assays [i.e., Ca 3 (PO 4 ) 2 and biotite dissolution assays and acidification assays] revealed phenotypic differences that depended on the carbon source, the bacterial strain, and the type of mineral. Four phenotypic patterns were observed: (i) high MWe activity associated with strong acidification and limited growth; (ii) in the tricalcium phosphate (TCP) assay only, moderate MWe activity beneath the colony associated with good bacterial growth; (iii) no MWe activity associated with the absence of acidification and strong growth; or (iv) complete absence of growth and MWe activity. These findings support a close relationship between carbon source utilization, bacterial metabolism, and MWe effectiveness. This work advances our understanding of bacterial mineral weathering, a dynamic process that plays a key role in long-term soil fertility and plant growth and whose effectiveness is influenced by multiple factors, including the nature of the mineral substrate.