Biosynthetic, genetic, taxonomic and functional diversity of glucose-dependent pyrroloquinoline quinone (PQQ) producing rhizobacteria

Pyrroloquinoline quinone (PQQ) is a versatile redox-active metabolite that exerts diverse physiological benefits across plant, animal and microbial systems. As PQQ biosynthesis is exclusive to bacteria, bioprospecting for efficient PQQ producers remains pivotal for ecological and future biotechnological investigations. The present study employed an integrated biochemical, genetic and phylogenetic approach to recover efficient PQQ-producing bacteria from rhizospheric soils. Using a dual selection strategy combining methanol utilization and phosphate (P) solubilisation, 80 rhizospheric isolates were screened to recover thirty PQQ producers, broadly classified as Firmicutes and Actinobacteria. Occurrence of key PQQ biosynthetic ( pqqA, B, C, E ) and glucose dehydrogenase-encoding genes supported the observed P-solubilizing potential. Substantial variability in PQQ yields across the isolates highlighted the putative influence of factors beyond genetic framework. Operational subcellular distribution indicated pre-dominant recovery of PQQ in the extracellular fraction. Under P-limitation, Glutamibacter nicotianae C2 exhibited the highest PQQ yield (~55.83 μg/ml), whereas Bacillus tequilensis D4 demonstrated highest biomass-normalized productivity (~339.7 μg/mg total protein); the yields being within the range reported for several industrially explored methylotrophic PQQ producing strains. Extracellular PQQ in representative isolates was confirmed using HR-LCMS/MS through detection of the precursor ion [M–H] − with m/z ~329.0051. Concurrent plant-beneficial traits including potassium solubilization, siderophore, indole-3-acetic acid and hydrogen cyanide production in B. tequilensis D4 suggest its potential for rhizospheric applications. Collectively, characterization of 30 rhizospheric PQQ-producers expands the current repertoire of reported PQQ-producing bacteria, highlights Gram-positive rhizobacteria as an underexplored source of PQQ producers, and provides a foundation for next-generation rhizosphere engineering and biomanufacturing applications.