Sphingomonas arvum sp. nov.: A promising microbial chassis for high-yield and sustainable zeaxanthin biomanufacturing

The yield of natural products from plants is currently insufficient and cannot be considered a sustainable and secure source of supply, especially given the challenges posed by global climate change. Therefore, a biofoundry that can quickly and accurately produce desired materials from microorganisms based on synthetic biology is urgently needed. Moreover, it is important to find new microbial and genetic chassis to meet the rapidly growing global market for high-value-added zeaxanthin. In this study, we aimed to identify the zeaxanthin biosynthetic gene cluster, crtZ-crtB-crtI-crtY, and confirm zeaxanthin production (11,330 μg g-1 dry biomass weight) through genome mining and liquid chromatography/mass spectrometry profiling using the novel zeaxanthin-producing bacteria Sphingomonas sp. strain BN140010T isolated from the subsurface soil of arable land. We report the highest yield among zeaxanthin-producing Sphingomonas strains to date. Moreover, we determined the taxonomic position of BN140010T using a polyphasic approach based on phylogenetic, physiological and chemotaxonomic characteristics, and we proposed Sphingomonas arvum strain BN140010T as a novel strain. Our results provide a zeaxanthin-producing chassis and diverse genetic tools for microbiological zeaxanthin production. Therefore, this research advances our progress towards the goal of lowering the unit cost of zeaxanthin production, making it more accessible for industrial applications.

Description and genomic characterization of Nocardioides bruguierae sp. nov., isolated from Bruguiera gymnorhiza

Strains BSK12Z-3^T and BSK12Z-4, two Gram-stain-positive, aerobic, non-spore-forming strains, were isolated from Shankou Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. The diagnostic diamino acid in the cell-wall peptidoglycan of strain BSK12Z-3^T was LL-diaminopimelic acid and MK-8(H₄) was the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phospholipid (PL). The major fatty acids was iso-C_16:0. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the two strains fell within the genus Nocardioides, appearing most closely related to Nocardioides ginkgobilobae KCTC 39594^T (97.5-97.6 % sequence similarity) and Nocardioides marinus DSM 18248^T (97.4-97.6 %). Genome-based phylogenetic analysis confirmed that strains BSK12Z-3^T and BSK12Z-4 formed a distinct phylogenetic cluster within the genus Nocardioides. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strains BSK12Z-3^T, BSK12Z-4 with their most related species N. marinus DSM18248^T were within the ranges of 77.2-77.3 % and 21.3-21.4 %, respectively, clearly indicated that strains BSK12Z-3^T, BSK12Z-4 represented novel species. Strains BSK12Z-3^T and BSK12Z-4 exhibited 99.9 % 16S rRNA gene sequence similarity. The ANI and dDDH values between the two strains were 97.8 % and 81.1 %, respectively, suggesting that they belong to the same species. However, DNA fingerprinting discriminated that they were not from one clonal origin. Based on phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizatons, strains BSK12Z-3^T and BSK12Z-4 could be classified as a novel species of the genus Nocardioides, for which the name Nocardioides bruguierae sp. nov., is proposed. The type strain is BSK12Z-3^T (=CGMCC 4.7709^T = JCM 34554^T).

Genomic Insight into Shimazuella Soli Sp. Nov. Isolated from Soil and Its Putative Novel Class II Lasso Peptide

The strain designated as AN120528^T was isolated from farmland soil in South Korea. This strain grows well on R2A medium at 28 °C. The cells are an off-white colour and have no hyphae. The phylogenetic analysis indicated that the strain is a member of the genus Shimazuella with a 98.11% similarity to Shimazuella alba KC615^T and a 97.05% similarity to S. kribbensis KCTC 9933^T, respectively. The strain AN120528^T shares common chemotaxonomic features with the other two type strains in the genus. It has MK-9 (H₄) and MK-10 (H₄) as its predominant menaquinones. The major fatty acids are iso-C_14:0, iso-C_15:0, anteiso-C_15:0 and iso-C_16:0. Diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), lipids (L), and aminolipids (AL) were identified as the major cellular polar lipids. Analysis of the peptidoglycan showed the presence of meso-diaminopimelic acid. Whole-genome sequencing revealed that the genome of the strain is approximately 3.3 Mbp in size. The strain showed a 77.5% average nucleotide identity (ANI) with S. alba KC615^T. The genomic DNA (gDNA) G + C content is 39.0%. Based on polyphasic taxonomy analysis, it is proposed that this strain, AN120528^T, represents a novel species in the genus Shimazuella, designated as Shimazuella soli sp. nov. The type stain is AN120528^T (=KCTC 39810^T = DSM 103571^T). Furthermore, shimazuellin I, a new 15-amino-acid peptide, was discovered in the AN120528^T through genome mining; it has the features of a lasso peptide, containing eight amino acids (-G-Q-G-G-S-N-N-D-) that form a macrolactam ring and seven amino acids (-D-G-W-Y-H-S-K-) that form a tail.