Changes in growth, lanthanide binding, and gene expression in Pseudomonas alloputida KT2440 in response to light and heavy lanthanides

Pseudomonas alloputida KT2440 is a ubiquitous, soil-dwelling bacterium that metabolizes recalcitrant and volatile carbon sources. The latter are utilized by two redundant, Ca- and lanthanide (Ln)-dependent, pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ ADH), PedE and PedH, whose expression is regulated by Ln availability. P. alloputida KT2440 is the best-studied, non-methylotroph in the context of Ln-utilization. We report the most comprehensive differential gene expression analysis, to date, for any Ln-utilizing microbe. Combined with microfluidic cultivation and single-cell elemental analysis, we studied the impact of light and heavy Ln when growing P. alloputida KT2440 with 2-phenylethanol as the carbon and energy source. Light Ln (La, Ce, Nd) and a mixture of light and heavy Ln (La, Ce, Nd, Dy, Ho, Er, Yb) had a positive effect on growth, while supplementation with heavy Ln (Dy, Ho, Er, Yb) exerted fitness costs. These were likely a consequence of mismetallation and oxidative stress. Gene expression analysis showed that the Ln sensing and signaling machinery, the two-component system PedS2R2 and PedH, responds differently to (non-)utilizable Ln. We broadened the understanding of the Ln switch in P. alloputida KT2440 and could show that it operates as a dimmer switch, modulating the pool of PQQ ADH dependent on Ln availability. Determined quantities of cell-associated Ln suggest a role for Ln beyond alcohol oxidation. The usability of Ln governs the response of P. alloputida KT2440 to different Ln elements. ImportanceThe Ln switch, the inverse regulation of Ca- and Ln-dependent PQQ ADH dependent on Ln availability in organisms featuring both, is central to our understanding of Ln utilization. Although the preference of bacteria for light Ln is well known, the effect of different Ln, light and heavy, on growth and gene expression has rarely been studied. We provide evidence for a dimmer switch-like regulation of Ca- and Ln-dependent PQQ ADH in P. alloputida KT2440, and could show that the response to (non-)utilizable Ln differs depending on the element. Ln commonly co-occur in nature. Our findings underline that Ln-utilizing microbes must be able to discriminate between Ln to use them effectively. Considering the prevalence of Ln-dependent proteins in many microbial taxa, more work addressing Ln sensing and signaling is needed. Ln availability likely necessitates different adaptations regarding Ln utilization.