Genomic sequence analysis of a plant-associated Photobacterium halotolerans MELD1: from marine to terrestrial environment?

Development of an Engineered Bacterial Endophyte: Promoting Plant Growth Through Pyrroloquinoline Quinone (PQQ) Synthesis

Endophytic bacteria are a group of microorganisms that can intercellularly colonize plant hosts without causing apparent damage or disease. Our previous works found that a pyrroloquinoline quinone (PQQ)-producing endophyte could promote plant growth and systemic tolerance. To demonstrate this PQQ-producing endophyte's beneficial role in plants, a set of five PQQ synthesis genes from Gluconobacter oxydans was introduced into both Escherichia coli JM109 and Bacillus subtilis RM125, a BsuM-deficient mutant of laboratory strain B. subtilis 168. Interestingly, both strains harboring the PQQ synthesis genes exhibited significantly higher optimal optical density than control strains. In a carbon flux analysis, both strains showed a noticeable increase in their citric acid, alpha-ketoglutaric acid, and succinic acid levels. Conversely, in E. coli, pyruvic acid, malic acid, and fumaric acid levels decreased. These results suggest that PQQ impacts various host species differently. Furthermore, the presence of PQQ in fermentation broth was also confirmed in the RM125 PQQ synthesis recombinant strain. Subsequent experiments by inoculating those Bacillus strains revealed that the laboratory host strain could function as an endophyte, and the PQQ transgenic strain could further promote the growth of Arabidopsis thaliana and increase the number of siliques. These findings confirm PQQ's vital role in endophyte-mediated plant growth promotion and also suggest the potential of B. subtilis transformed with PQQ genes as an engineered endophyte for studying PQQ's biological functions in plants. This research is a step forward in understanding how specific substances can beneficially influence plant growth and systemic tolerance through endophytic mechanisms.

Characterization of the Pyrroloquinoline Quinone Producing Rhodopseudomonas palustris as a Plant Growth-Promoting Bacterium under Photoautotrophic and Photoheterotrophic Culture Conditions

Rhodopseudomonas palustris is a purple non-sulfide bacterium (PNSB), and some strains have been proven to promote plant growth. However, the mechanism underlying the effect of these PNSBs remains limited. Based on genetic information, R. palustris possesses the ability to produce pyrroloquinoline quinone (PQQ). PQQ is known to play a crucial role in stimulating plant growth, facilitating phosphorous solubilization, and acting as a reactive oxygen species scavenger. However, it is still uncertain whether growth conditions influence R. palustris's production of PQQ and other characteristics. In the present study, it was found that R. palustris exhibited a higher expression of genes related to PQQ synthesis under autotrophic culture conditions as compared to acetate culture conditions. Moreover, similar patterns were observed for phosphorous solubilization and siderophore activity, both of which are recognized to contribute to plant-growth benefits. However, these PNSB culture conditions did not show differences in Arabidopsis growth experiments, indicating that there may be other factors influencing plant growth in addition to PQQ content. Furthermore, the endophytic bacterial strains isolated from Arabidopsis exhibited differences according to the PNSB culture conditions. These findings imply that, depending on the PNSB's growing conditions, it may interact with various soil bacteria and facilitate their infiltration into plants.

Comparative Genomic Analyses of the Genus Photobacterium Illuminate Biosynthetic Gene Clusters Associated with Antagonism

The genus Photobacterium is known for its ecophysiological versatility encompassing free-living, symbiotic, and pathogenic lifestyles. Photobacterium sp. CCB-ST2H9 was isolated from estuarine sediment collected at Matang Mangrove, Malaysia. In this study, the genome of CCB-ST2H9 was sequenced, and the pan-genome of 37 Photobacterium strains was analysed. Phylogeny based on core genes showed that CCB-ST2H9 clustered with P. galatheae, forming a distinct clade with P. halotolerans, P. salinisoli, and P. arenosum. The core genome of Photobacterium was conserved in housekeeping functions, while the flexible genome was well represented by environmental genes related to energy production and carbohydrate metabolism. Genomic metrics including 16S rRNA sequence similarity, average nucleotide identity, and digital DNA–DNA hybridization values were below the cut-off for species delineation, implying that CCB-ST2H9 potentially represents a new species. Genome mining revealed that biosynthetic gene clusters (BGCs) involved in producing antimicrobial compounds such as holomycin in CCB-ST2H9 could contribute to the antagonistic potential. Furthermore, the EtOAc extract from the culture broth of CCB-ST2H9 exhibited antagonistic activity against Vibrio spp. Intriguingly, clustering based on BGCs profiles grouped P. galatheae, P. halotolerans, P. salinisoli, P. arenosum, and CCB-ST2H9 together in the heatmap by the presence of a large number of BGCs. These BGCs-rich Photobacterium strains represent great potential for bioactive secondary metabolites production and sources for novel compounds.

Lagierella massiliensis gen. nov., sp. nov., Isolated from a Stool Sample

Strain Marseille-P2012^T was described to represent a new bacterial genus belonging to the phylum Firmicutes using the taxonogenomics concept. It was isolated from stool samples of a healthy 2-year-old Senegalese boy in a study of the human gut microbiota. This strain is a Gram-positive, anaerobic, non-motile and coccus-shaped bacterium. The 16S rRNA gene sequence of strain Marseille-P2012 exhibited 90.5% similarity with Finegoldia magna strain ATCC 29,328, the phylogenetically closest species with standing in nomenclature. The genome of strain Marseille-P2012^T is 1,832,315 bp-long with 32.46 mol% of G + C content. With regard to its phenotypic, biochemical and genomic characteristics, this bacterium was classified as a new bacterial genus and species, Lagierella massiliensis gen. nov., sp. nov., with strain Marseille-P2012^T (= CSUR P2012 = DSM100854) as type strain.