Mining the Galium aparine L. microbiome: genome-guided discovery and experimental validation of...

Environmental pollution resulting from heavy metals constitutes a critical global issue. Remediation technologies offer potential solutions, particularly through the innovative use of endophytic microbes, either independently or in conjunction with plants. This solution is based on the ability of certain endophytic bacteria to produce metallophores, which are low-molecular-weight compounds capable of chelating various heavy metals.

This study investigates ten bacterial endophytes isolated from the medicinal plant Galium aparine L. belonging to the Bacillus, Priestia, and Peribacillus genera. We tested different media to efficiently induce their production and assessed their ability to chelate various heavy metals, including highly toxic Pb²⁺, Cd²⁺ and Hg²⁺. Moreover, we examined in detail of their metallophore gene clusters, their organization, diversity and prevalence, by broad homology search.

All strains exhibited moderate to high metallophore production ability, with few strains capable of chelating more metals than iron. Among them, Priestia sp. GS2 was identified as promising producer, reaching up to 60% SU, with binding activity also towards Co²⁺, Mn²⁺, Zn²⁺, Ni²⁺ or Cu²⁺. Also, Peribacillus frigoritolerans GR2 exhibits a remarkable ability to chelate Pb²⁺, Hg²⁺ and Cd²⁺. An in-depth analysis of the biosynthetic gene clusters and enzymes involved in metallophore biosynthesis revealed homologous clusters within previously deposited genomes, highlighting their distribution and potential evolutionary conservation.

The strains demonstrated capacity for metallophore production and heavy metal chelation, which makes them promising candidates for the development of advanced microbial solutions. A genome-guided selection approach can guide the selection of strains for agricultural applications, where they enhance plant nutrient uptake, suppress soil pathogens, and support sustainable fertilization strategies beyond sequestering crucial metals. Apart from agriculture, purified metallophores can aid bioremediation and mobilization of heavy metals from various environments and matrices.