Isolation of diverse Undibacterium-related strains from alpine lakes and re-examining the taxonomic status of this genus

Abstract

The genus Undibacterium is an important member of Oxalobacteraceae and most species of this genus were isolated from freshwater environments. The recent study based on the genomic analyses revised the taxonomic status of 23 Undibacterium species and proposed that these species should be assigned into four genera (Undibacterium, Neoundibacterium, Affinundibacterium and Paraundibacterium), respectively. During the investigation of microbial resources inhabited in alpine lakes from the southwestern China in 2023, 25 strains show the highest 16S rRNA gene sequence similarities with Undibacterium species were isolated. Utilizing the genomes of these 25 strains and 26 Undibacterium species, the phylogenies among these strains are reconstructed based on the core and pan-genome, respectively. The phylogenomic trees show that the 26 Undibacterium species should be divided into six clades and each clade should represent an independent genus. As the clades 2, 3, 4 and 5 proposed in this study have been revised in other study, the genera Cognatundibacterium and Pseudundibacterium are proposed in this study to accommodate the clades 1 and 6, respectively. The detailed genomic annotations reveal that all the 25 isolated Undibacterium-related strains harbor complete amino acids metabolisms and genes encoding DNA replication and repair, homologous recombination proteins, two-component and phosphate transport systems in response to the oligotrophic, high UV radiation and phosphorus-limited environments of alpine lakes. This study clarifies the role of Undibacterium-related strains in alpine lakes and demonstrates that isolating more strains is of great benefit to the bacterial taxonomy.