Chromobacterium indicum sp. nov., a Pigment-Producing Bacterium Isolated from Soil

Area of Science:

• Microbiology
• Bacteriology
• Genomics

Background:

• The genus Chromobacterium comprises Gram-negative bacteria known for producing violacein pigment.
• Accurate taxonomic classification is crucial for understanding microbial diversity and function.

Purpose of the Study:

• To characterize a novel purple-pigmented bacterial isolate from a tea garden soil sample.
• To determine the taxonomic status of the isolate using polyphasic characterization, including genomic and phenotypic analyses.

Main Methods:

• Isolation and cultivation of the bacterial strain TRC1.1.SA^T.
• Gram staining, motility tests, and assessment of oxidase and catalase activities.
• 16S rRNA gene sequencing and whole-genome sequencing for phylogenetic analysis.
• Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) for genomic relatedness.
• Analysis of polar lipids and fatty acid profiles.
• Identification of biosynthetic gene clusters (BGCs) using RAST and antiSMASH.

Main Results:

• Strain TRC1.1.SA^T is a Gram-negative, rod-shaped, motile bacterium growing aerobically between pH 5.0-9.0 and 15-37 °C.
• 16S rRNA gene sequence analysis showed high similarity to Chromobacterium piscinae, C. vaccinii, and C. violaceum.
• Genomic analyses (ANI < 96% and dDDH < 63.4%) indicated significant divergence from known Chromobacterium species.
• The genome contains a BGC for violacein pigment production.
• Major polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, and phosphoglyceraldehyde; major fatty acids were C_16:0, C_16:1ω7c, C_17:0 cyclo, and C_18:1ω7c.

Conclusions:

• Strain TRC1.1.SA^T represents a novel species within the genus Chromobacterium based on distinct genomic and phenotypic characteristics.
• The proposed name for the novel species is Chromobacterium indicum.
• The type strain is designated TRC1.1.SA^T (MTCC 13391^T; JCM 36723^T; KCTC 8324^T).