Isolation and characterization of a novel strain, Paenibacillus lacisediminis sp. nov., exhibiting both biomacromolecule degradation and plant growth-beneficial activities

The Paenibacillus srains exhibit diverse abilities to secrete hydrolases capable of degrading biomacromolecules and to act as plant growth-promoting bacteria (PGPB) through the degradation of fungal cell walls and promotion the nutrient cycling of nitrogen (N) and phosphorus (P). Despite the well-acknowledged attributes of Paenibacillus, only limited studies have identified strains of it concurrently produce multiple hydrolytic enzymes and display strong phytobeneficial characteristics. The objective of this study was to isolate and functionally characterize a novel Paenibacillus strain that combines hydrolytic capabilities with plant growth-promoting potential. Strain TH7-28T was isolated and taxonomically classified through a polyphasic identification approach based on 16S rRNA gene phylogeny, genome analysis, and physiological and biochemical characteristics. Its metabolic capabilities were characterized using CAZy and KEGG pathway annotations, supplemented by Kofam-KOALA functional profiling. Genomic relatedness to reference strains was determined using OGRIs: ANI, dDDH, and tetra-nucleotide frequency signature analyses. Biophysical and biochemical properties were evaluated through enzymatic activity assays, antimicrobial susceptibility testing, respiratory quinone system identification, fatty acid methyl ester profiling, and polar lipid composition analysis. The wheat germination test was used to verify the plant growth-promoting ability. Strain TH7-28T was Gram-stain-positive, aerobic, white and rod-shaped. Phylogenetic analysis based on the 16S rRNA gene and genomic sequence indicated that strain TH7-28T was classified within the genus Paenibacillus. The ANI values of strain TH7-28T with the closest related strains P. macerans ATCC 8244T and P. oralis KCOM 3021T were 91.00% and 92.85%, respectively. The dDDH values of strain TH7-28T with P. macerans ATCC 8244T and P. oralis KCOM 3021T were 44.60% and 52.40%, respectively. The respiratory quinone was menaquinone 7 (MK-7). The major cellular fatty acids (> 10%) comprised anteiso-C15:0, anteiso-C17:0, iso-C16:0 and C16:0. The genomic DNA G + C content was 52.1%. Phosphatidylethanolamine, two amino lipids and three phospholipids were the main polar lipids. Genomic sequencing revealed multifunctional gene clusters encoding carbohydrate-active enzymes (cellulase and amylase), proteases, and phospholipases, alongside antifungal chitinase and endo-β-1,3-glucanase. The biomolecular metabolic gene types and gene copy numbers of strain TH7-28T were significantly higher than those of other Paenibacillus genus, indicating its robust capacity for macromolecule degradation. The nitrogen-fixing potential of strain TH7-28T was confirmed via nifH/D/K genes. Phosphorus activation capacity was demonstrated through pstS/C/A/B-mediated inorganic uptake and phospholipase-driven organic solubilization. Experimental assays further demonstrated significant enzymatic activities of chitinase (8.12 ± 0.66 × 10–3 U/mL), β-1,3-glucanase (0.023 ± 0.004 U/mL), and nitrogenase (0.164 ± 0.006 U/mL), with concurrent hydrolysis of cellulose, starch, casein, chitin and lecithin. Through the wheat germination experiment, it has been confirmed that this strain significantly enhanced both the seed germination rate and stem length, thereby establishing a solid foundation for subsequent research on its practical applications. Strain TH7-28T, isolated from lake sediment, was identified to represent a novel species designated Paenibacillus lacisediminis sp. nov. The strain exhibits multifunctional hydrolase activities, antifungal enzyme synthesis, nitrogen fixation, phosphorus solubilization and plant growth promoting. The findings confirm Paenibacillus lacisediminis sp. nov. as a biotechnologically promising strain for sustainable agriculture, furthermore enriching the functional repertoire of Paenibacillus genus.