Unveiling the cadmium tolerance mechanisms of endophytic PGPB Pantoea sp. EEL5 isolated from Thinopyrum elongatum and its bioremediation for acidic cadmium-contaminated soil.

Cadmium (Cd) contamination in acidic soils poses a critical threat to agricultural productivity and safety. However, effective microbial strategies remain challenging due to the scarcity of microbial resources that are dual-resistant to acid and Cd. Here, we investigated the Cd-resistance mechanisms of Pantoea sp. EEL5, an acid- and Cd-tolerant plant growth-promoting bacterium, and evaluated its potential to remediate acidic Cd-contaminated soil. EEL5 exhibited efficient Cd2 + removal through extracellular adsorption and intracellular accumulation. Transcriptomic and biochemical analyses revealed that EEL5 utilizes multiple mechanisms to withstand stress: enhancing respiratory chain activity for energy supply; inhibiting type-I NADH dehydrogenase to curb reactive oxygen species generation, while inducing a manganese superoxide dismutase (Mn-SOD)- and Thioredoxin/Peroxiredoxin-centered antioxidant system for scavenging; and activating sulfur metabolism to boost hydrogen sulfide and glutathione production for detoxification, alongside stimulating Cd2+ efflux. In acidic Cd-contaminated soil, EEL5 colonization markedly improved the soil environment by elevating pH, reducing soluble Cd, and enhancing soil enzyme activities and nutrient (NH4+-N, phosphorus, and sulfur) availability. Microbiome analysis revealed that EEL5 drove a specific functional guild shift: it enriched proton-consuming nitrogen transformers (dissimilatory nitrate reduction to ammonium (DNRA) bacteria, ammonifiers, fixers) over acid-producing nitrifiers, thereby acting as a primary biological driver for neutralizing soil acidity. Concurrently, EEL5 recruited synergistic Cd-immobilizing partners (Magnetospirillum, Myxococcus). Correlation analysis confirmed that these microbial successions were pivotal for driving pH elevation and Cd sequestration. Overall, these findings advance the mechanistic understanding of Cd tolerance in Pantoea, and highlight EEL5 as a promising microbial resource for developing safe and effective strategies to remediate acidic Cd-contaminated soils.