Sphingomonas incarnata sp. nov., an endophytic bacterium with bioactive potential isolated from passionfruit leaves

The genus Sphingomonas encompasses metabolically versatile bacteria found in diverse environments; however, species associated with the leaf endosphere of medicinal plants remain poorly characterized. Here we describe a novel species isolated from the leaf endosphere of Passiflora incarnata, a medicinal plant recognized for its rich content of flavonoids and phenolic compounds, collected in São Paulo, Brazil.

A Gram-negative, aerobic, rod-shaped, motile bacterium, designated strain EP61.1^T, was characterized through a polyphasic taxonomic approach. Genome-based indices confirmed species-level distinctiveness, with average nucleotide identity values ranging from 85.50 to 92.37% and digital DNA-DNA hybridization values from 22.8 to 45.8%, both below the accepted thresholds for prokaryotic species delineation. The genome comprises 4.82 Mbp with a guanine-cytosine content of 67.83%, encoding 4,479 protein-coding sequences. The predominant respiratory quinone is ubiquinone Q-10; the major cellular fatty acids are summed feature 8 (C18:1 ω7c/C18:1 ω6c) and C16:0; and the polar lipid profile includes diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, sphingoglycolipid, glycolipids, phosphoaminolipids, and two unidentified lipids. Biosynthetic gene clusters such as zeaxanthin (a photoprotective carotenoid) and siderophores (iron-chelating compounds) were predicted from the genome. Additionally, volatile organic compounds produced by strain EP61.1^T promoted plant growth and induced flavonoid accumulation in Arabidopsis thaliana seedlings under controlled conditions.

Based on polyphasic taxonomic evidence, strain EP61.1^T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas incarnata sp. nov. is proposed. The predicted biosynthetic gene clusters suggest ecological advantages underlying its endophytic lifestyle, while the capacity to modulate plant secondary metabolism through interkingdom volatile signaling points to broader relevance for plant health and biotechnological applications. The type strain is EP61.1^T (= CBMAI 2297^T = ICMP 24843^T = MUM 23.02^T).