Novel gut bacteria species Paenibacillus ilasis with phosphorus degrading and soluble starch hydrolysis abilities isolated from fresh feces of rhinoceros

Abstract

The genus Paenibacillus, known for its diverse sources, is a valuable reservoir of antimicrobial compounds, enzymes and other valuable chemicals, with applications in medicine, agriculture, and bioremediation. Despite this, Paenibacillus strains, particularly those isolated from unique environments, remain underexplored, limiting our understanding of their potential, capabilities and taxonomic classifications. The gut microbiome of large herbivores, such as rhinoceroses, harbors underexplored microbial diversity with unique metabolic capabilities. In this study, a Gram-stain-negative, facultatively aerobic, motile, spore-forming, rod-shaped bacterial strain, NGMCC 1.200843^T (= CGMCC 1.64763^T = JCM 37214^T), was isolated from fresh rhinoceros feces and characterized its taxonomic status and metabolic potential. Phylogenetic, phenotypic, and chemotaxonomic analyses confirmed the isolate as a novel species within the genus Paenibacillus, closely related to Paenibacillus lautus DSM 3035^T (98.62% 16S rRNA gene similarity). The average nucleotide identity (ANI) and the digital DNA-DNA hybridization values were below the threshold for species delineation. The major cellular fatty acids were anteiso-C_15:0, C_16:0 and iso-C_16:0 (> 10%) and the polar lipid profile contained diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), two unidentified phospholipids (PL1-2) and one phosphatidyl choline (PC). The total DNA G + C content was 49.69 mol%. The isolate exhibited significant phosphate solubilization and starch hydrolysis activities in plate assays, suggesting a role in nutrient cycling within the rhinoceros gut. We propose the name Paenibacillus ilasis sp. nov. for this strain. These findings enhance our understanding of gut microbial diversity in herbivores and lay the foundation for future applications in agriculture or industry.

Keywords: Paenibacillus ilasis sp. nov.; Organophosphorus solubilization; Polyphasic taxonomy; Soluble starch hydrolysis.

Fig. 1

Scanning electron micrograph of strain NGMCC 1.200843^T. Bar = 1.0 μm.

Fig. 2

Polar lipids profile of strain NGMCC 1.200843^T after two-dimensional TLC and detection with (A) molybdophosphoric aicd, (B) ninhydrin, (C) α-naphthol and (D) molybdenum blue. DPG diphosphatidylglycerol, PG phosphatidylglycerol, PE phosphatidylethanolamine, PL1-2 unidentified phospholipids, PC phosphatidyl choline.

Fig. 3

Maximum likelihood (ML) phylogenetic tree of strains NGMCC 1.200843^T with other type strains within Paenibacillus genus. Bacillus subtilis subsp. Virginiana HUB-1-047^T (GQ892930) is used as the outgroup. Numbers at nodes (bootstrap values) indicate percentages of 1000 replications and are shown where > 50%. Bar, 0.1 substitutions per nucleotide position.

Fig. 4

Genome phylogenomic tree showing the position of strain NGMCC 1.200843^T. Bootstrap values are indicated at branch points based on 1000 iterations. Bacillus subtilis DSM 10^T (NZ_JAEPVU010000011.1) was used as an outgroup. Bar, 0.1 substitutions per nucleotide position.

Fig. 5

Qualitative analysis of organic P solubilization ability. (A) Escherichia coli L-7 as negative control; (B) Strain NGMCC 1.200843^T cultivated on lecithin as P source medium plates.

Fig. 6

Qualitative analysis of starch hydrolysis ability by iodine staining on starch agar plates. The presence of a clear zone around culture growth indicates positive starch hydrolysis. (A,B) Escherichia coli L-7 as negative control, starch-hydrolytic activity before and after iodine application. (C,D) the positive starch hydrolytic activity of NGMCC 1.200843^T before and after addition of iodine solution.

Fig. 7

Genomic analysis of stain NGMCC 1.200843^T. (A) KEGG function classification; (B) CAZy function classification; (C) COG function classification; (D) GO function classification.