Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity

Abstract

Advances in the computational annotation of genomes and the predictive potential of current metabolic models, based on more than thousands of experimental phenotypes, allow them to be applied to identify the diversity of metabolic pathways at the level of ecophysiology differentiation within taxa and to predict phenotypes, secondary metabolites, host-associated interactions, survivability, and biochemical productivity under proposed environmental conditions. The significantly distinctive phenotypes of members of the marine bacterial species Pseudoalteromonas distincta and an inability to use common molecular markers make their identification within the genus Pseudoalteromonas and prediction of their biotechnology potential impossible without genome-scale analysis and metabolic reconstruction. A new strain, KMM 6257, of a carotenoid-like phenotype, isolated from a deep-habituating starfish, emended the description of P. distincta, particularly in the temperature growth range from 4 to 37 °C. The taxonomic status of all available closely related species was elucidated by phylogenomics. P. distincta possesses putative methylerythritol phosphate pathway II and 4,4′-diapolycopenedioate biosynthesis, related to C30 carotenoids, and their functional analogues, aryl polyene biosynthetic gene clusters (BGC). However, the yellow-orange pigmentation phenotypes in some strains coincide with the presence of a hybrid BGC encoding for aryl polyene esterified with resorcinol. The alginate degradation and glycosylated immunosuppressant production, similar to brasilicardin, streptorubin, and nucleocidines, are the common predicted features. Starch, agar, carrageenan, xylose, lignin-derived compound degradation, polysaccharide, folate, and cobalamin biosynthesis are all strain-specific.

Genome‐based taxonomic analysis of the genus Pseudoalteromonas reveals heterotypic synonyms

“…While preparing this article, a study was published wherein the P. elyakovii VKPM B‐3905 T genome was presented (Balabanova et al, 2023). Unexpectedly, the newly sequenced isotype did not cluster with the other two P. elyakovii type strain genomes and was sister to P. shioyasakiensis JCM 18891 T in the phylogenomic tree (Figure 1).…”

Chitinolytic and Fungicidal Potential of the Marine Bacterial Strains Habituating Pacific Ocean Regions

“…The 16S rRNA gene sequence comparison of these highly active chitinolytics with the type strains in the EzBioCloud database showed that eight strains, Sgf 25, Sgm 25/1, Sh 1, Sh 2, Sh 3, Sh 4, Sh 5, and 14G-22, belong to the genus Microbulbifer (family Microbulbiferaceae of the phylum Proteobacteria ); three strains, Sgm 5, Sgm 22, and 14G-20, are representatives of the genus Vibrio (family Vibrionaceae of the phylum Proteobacteria ); the strain V1SW 51 is related to the genus Aquimarina (family Flavobacteriaceae of the phylum Bacteroidetes ); and the strain B530 belongs to the genus Pseudoalteromonas (family Pseudoalteromonadaceae of the phylum Proteobacteria ) [ 42 ]. However, the Vibrio and Pseudoalteromonas isolates have the plural polymorphic 16S rRNA genes that make their species identification difficult without thorough genome-based or species-specific analysis [ 43 , 44 ].…”

Biotechnological Key Genes of the Rhodococcus erythropolis MGMM8 Genome: Genes for Bioremediation, Antibiotics, Plant Protection, and Growth Stimulation

“…The biosynthetic gene clusters (BGCs) displaying 75% similarity encompass various functionalities, including the synthesis of compounds responsible for membrane fluidity maintenance, branched-chain fatty acids, and the osmolyte ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidine carboxylic acid), which is vital for halophilic microorganism adaptation [ 39 , 40 ]. Notably, ectoine serves as a structural component facilitating survival under unfavorable conditions, with its presence confirmed in the genome of R. erythropolis MGMM8.…”