Genome mining revealed polyhydroxybutyrate biosynthesis by Ramlibacter agri sp. nov., isolated from agriculture soil in Korea

The Bacterial Genus Ramlibacter: Betaproteobacteria Capable of Surviving in Oligotrophic Environments Thanks to Several Shared Genetic Adaptation Traits

Ramlibacter tataouinensis, the type species of the genus Ramlibacter, is renowned for its ability to thrive in hot, arid and nutrient-poor desert soils. To investigate whether its adaptive properties are shared across all 20 currently described Ramlibacter species found in diverse terrestrial and aquatic habitats worldwide, we conducted a comprehensive analysis of 16S rRNA sequences and genomic information available from the literature. Our study encompassed approximately 40 deposited genomes, allowing us to propose a genomic phylogeny that aligns with the 16S rRNA phylogeny. Our findings reveal several conserved features across the genus Ramlibacter. This includes the presence of light sensors, environmental sensing networks, organic carbon and phosphate acquisition systems and the ability to store carbon and energy in the form of polyhydroxyalkanoate or polyphosphate granules. These shared traits rationalise the widespread distribution of Ramlibacter in oligotrophic terrestrial and aquatic environments. They also explain the genus' ability to withstand desiccation, endure extended periods of starvation, and survive in nutrient-depleted conditions. Notably, certain adaptive features are further enhanced in several species by their pleiomorphism and ability to form cysts. Overall, our study not only highlights the ecological adaptations of Ramlibacter species but also extends our understanding of microbial ecology in oligotrophic environments.

Novel 4-chlorophenoxyacetate dioxygenase-mediated phenoxyalkanoic acid herbicides initial catabolism in Cupriavidus sp. DL-D2

Microbial metabolism is an important driving force for the elimination of 4-chlorophenoxyacetic acid residues in the environment. The α-Ketoglutarate-dependent dioxygenase (TfdA) or 2,4-D oxygenase (CadAB) catalyzes the cleavage of the aryl ether bond of 4-chlorophenoxyacetic acid to 4-chlorophenol, which is one of the important pathways for the initial metabolism of 4-chlorophenoxyacetic acid by microorganisms. However, strain Cupriavidus sp. DL-D2 could utilize 4-chlorophenoxyacetic acid but not 4-chlorophenol for growth. This scarcely studied degradation pathway may involve novel enzymes that has not yet been characterized. Here, a gene cluster (designated cpd) responsible for the catabolism of 4-chlorophenoxyacetic acid in strain DL-D2 was cloned and identified, and the dioxygenase CpdA/CpdB responsible for the initial degradation of 4-chlorophenoxyacetic acid was successfully expressed, which could catalyze the conversion of 4-chlorphenoxyacetic acid to 4-chlorocatechol. Then, an aromatic cleavage enzyme CpdC further converts 4-chlorocatechol into 3-chloromuconate. The results of substrate degradation experiments showed that CpdA/CpdB could also degrade 3-chlorophenoxyacetic acid and phenoxyacetic acid, and homologous cpd gene clusters were widely discovered in microbial genomes. Our findings revealed a novel degradation mechanism of 4-chlorophenoxyacetic acid at the molecular level.

Ramlibacter paludis sp. nov., isolated from wetland

A Gram-stain-negative, non-motile, rod-shaped, aerobic and white-coloured bacterium (designated XY19^T) was isolated from a soil sample of wetland from Godeok Ecological Park, Gangdong-gu, Seoul, Republic of Korea. On the basis of 16S rRNA gene sequencing, strain XY19^T clustered with species of the genus Ramlibacter and appeared closely related to R. ginsenosidimutans DSM 23480^T (98.42 %), R. alkalitolerans JCM 32081^T (97.68 %) and R. monticola JCM 31918^T (97.66 %). The average nucleotide identity between strain XY19^T and three strains (R. ginsenosidimutans DSM 23480^T, R. alkalitolerans JCM 32081^T and R. monticola JCM 31918^T) were 80.7, 81.1 and 81.4 %. And the digital DNA-DNA hybridization (dDDH) calculated between strain XY19^T and each of the three strains (R. ginsenosidimutans DSM 23480^T, R. alkalitolerans JCM 32081^T and R. monticola JCM 31918^T) were 24.1, 24.4 and 24.5 %. ANI value and dDDH results were a novel species of the genus Ramlibacter. Growth occurs at 10-37 °C on R2A medium in the pressence of 0-1 % NaCl (w/v) and at pH 6.0-8.5. The DNA G+C content of the genomic DNA was 68.7 mol%, and ubiquinone-8 (Q-8) was the major respiratory quinone. The major cellular fatty acids (>5 %) were C_16:1  ω7c and/or C_16:1 ω6c (summed feature 3), C_16 : 0, C_17 : 0 cyclo and C_18:1  ω7c and/or C_18:1  ω6c (summed feature 8). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified lipids and unidentified aminophospholipid. Physiological and biochemical characteristics indicated that strain XY19^T represents a novel species of the genus Ramlibacter, for which the name Ramlibacter paludis sp. nov. is proposed. The type strain is XY19^T (= KACC 22220^T = LMG 32190^T).