Saccharopolyspora karakumensis sp. nov., Saccharopolyspora elongata sp. nov., Saccharopolyspora aridisoli sp. nov., Saccharopolyspora terrae sp. nov. and their biotechnological potential revealed by genome analysis

Saccharopolyspora mangrovi sp. nov., a novel mangrove soil actinobacterium with distinct metabolic potential revealed by comparative genomic analysis

A novel mangrove soil-derived actinomycete, strain S2-29T, was found to be most closely related to Saccharopolyspora karakumensis 5K548T based on 16 S rRNA sequence (99.24% similarity) and genomic phylogenetic analyses. However, significant divergence in digital DNA-DNA hybridization, average nucleotide identity, and unique biosynthetic gene cluster possession distinguished S2-29T as a distinct Saccharopolyspora species. Pan genome evaluation revealed exceptional genomic flexibility in genus Saccharopolyspora, with > 95% accessory genome content. Strain S2-29T harbored 718 unique genes, largely implicated in energetic metabolisms, indicating different metabolic capacities from its close relatives. Several uncharacterized biosynthetic gene clusters in strain S2-29T highlighted the strain's untapped capacity to produce novel functional compounds with potential biotechnological applications. Designation as novel species Saccharopolyspora mangrovi sp. nov. (type strain S2-29T = JCM 34,548T = CGMCC 4.7716T) was warranted, expanding the known Saccharopolyspora diversity and ecology. The discovery of this mangrove-adapted strain advances understanding of the genus while highlighting an untapped source of chemical diversity.

BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets

Genome mining is revolutionizing natural products discovery efforts. The rapid increase in available genomes demands comprehensive computational platforms to effectively extract biosynthetic knowledge encoded across bacterial pangenomes. Here, we present BGCFlow, a novel systematic workflow integrating analytics for large-scale genome mining of bacterial pangenomes. BGCFlow incorporates several genome analytics and mining tools grouped into five common stages of analysis such as: (i) data selection, (ii) functional annotation, (iii) phylogenetic analysis, (iv) genome mining, and (v) comparative analysis. Furthermore, BGCFlow provides easy configuration of different projects, parallel distribution, scheduled job monitoring, an interactive database to visualize tables, exploratory Jupyter Notebooks, and customized reports. Here, we demonstrate the application of BGCFlow by investigating the phylogenetic distribution of various biosynthetic gene clusters detected across 42 genomes of the Saccharopolyspora genus, known to produce industrially important secondary/specialized metabolites. The BGCFlow-guided analysis predicted more accurate dereplication of BGCs and guided the targeted comparative analysis of selected RiPPs. The scalable, interoperable, adaptable, re-entrant, and reproducible nature of the BGCFlow will provide an effective novel way to extract the biosynthetic knowledge from the ever-growing genomic datasets of biotechnologically relevant bacterial species.

Saccharopolyspora ipomoeae sp. nov., an Actinomycete Isolated from Sweet Potato Field Soils

During the course of the isolation of actinobacteria from sweet potato field soils collected from Phra Nakhon Si Ayutthaya province of Thailand, strain TS4A08T was isolated and subjected to a polyphasic taxonomic approach. The 16S rRNA gene sequence analysis of strain TS4A08T revealed that it is closely related to the type strains of Saccharopolyspora aridisoli, and Saccharopolyspora endophytica with 98.7%, and 98.6% similarity, respectively. However, phylogenetic analyses using 16S rRNA gene and genome sequences indicated that strain TS4A08T clustered with Saccharopolyspora flava AS4.1520T (98.2% similarity), well-supported by bootstrap values, and formed distinct line from the two closest strains. The average nucleotide identity (ANI) values and digital DNA-DNA hybridization (dDDH) values between the genome sequences of strain TS4A08T and the closest type strains of S. aridisoli, S. endophytica, and S. flava, were 86.1-93.2% and 33.1-49.6%, respectively, which were less than the threshold for the species delineation. The genome size and the DNA G + C content of strain TS4A08T were 6.6 Mbp and 70.5%, respectively. The strain grew well at 25-37 °C, pH range of 7-9, and NaCl concentration of 0-5% (w/v). Whole-cell hydrolysates contained meso-diaminopimelic acid. The major fatty acids were iso-C16:0, anteiso-C17:0, and iso-C15:0. Strain TS4A08T exhibited phosphatidylcholine in its polar lipid profile, with MK-9(H4) being the predominant isoprenologue. The strain exhibits typical chemotaxonomic properties of the genus Saccharopolyspora, including arabinose, galactose, and ribose as whole-cell sugars. Strain TS4A08T represents a novel species within the genus Saccharopolyspora, for which the name Saccharopolyspora ipomoeae sp. nov. is proposed. The type strain is TS4A08T (= TBRC 17271T = NBRC 115967T).

Polyphasic characterization and genomic insights into Nocardioides turkmenicus sp. nov. isolated from a desert soil

Strain KC13T, a novel desert-adapted, non-motile, Gram-stain-positive, rod-shaped, aerobic bacterium, was isolated from a soil sample collected from the Karakum Desert, Turkmenistan and characterised by a polyphasic approach. Phylogenetic analysis based on 16S rRNA sequences revealed that strain KC13T was a member of the genus Nocardioides, and formed a distinct cluster with Nocardioides luteus DSM 43366T (99.3% sequence identity), Nocardioides albus DSM 43109T (98.9%), Nocardioides panzhihuensis DSM 26487T (98.3%) and Nocardioides albertanoniae DSM 25218T (97.9%). The orthologous average nucleotide identity and digital DNA-DNA hybridization values were in the range of 85.8-91.0% and 30.2-35.9%, respectively, with the type strains of closely related species. The genome size of strain KC13T was 5.3 Mb with a DNA G + C content of 69.7%. Comprehensive genome analyses showed that strain KC13T, unlike its close relatives, had many genes associated with environmental adaptation. Strain KC13T was found to have chemotaxonomic and phenotypic characteristics of members of the genus Nocardioides and some differences from phylogenetic neighbours. Based on the chemotaxonomic, genomic, phenotypic and phylogenetic data, strain KC13T represents a novel species of the genus Nocardioides, for which the name Nocardioides turkmenicus sp. nov. is proposed, and the type strain is KC13T (= JCM 33525T = CGMCC 4.7619T).

Saccharopolyspora oryzae sp. nov., isolated from rhizosphere soil of the wild rice species Oryza rufipogon

A novel actinobacterium, designated as strain WRP15-2T, was isolated from rhizosphere soil of rice plant (Oryza rufipogon). The strain was Gram-stain-positive, aerobic, and non-motile. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain WRP15-2T fell into the genus Saccharopolyspora. The strain shared the highest 16S rRNA gene sequence similarity with the type strains Saccharopolyspora kobensis JCM 9109T (99.1%), Saccharopolyspora indica VRC122T (98.9%), and Saccharopolyspora antimicrobica DSM 45119T (98.7%). However, the digital DNA-DNA hybridization and average nucleotide identity values among these strains confirmed that the microorganism represented a novel member of the genus Saccharopolyspora. Chemotaxonomic data revealed that strain WRP15-2T possessed MK-9(H4) as the predominant menaquinone. It contained meso-diaminopimelic acid as the diagnostic diaminopimelic acid and arabinose, galactose, and ribose as predominant whole-cell sugars. The detected phospholipids were dominated by phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxy-phosphatidylmethylethanolamine, and phosphatidylcholine. The predominant cellular fatty acids were iso-C16:0, C16:0, and iso-C15:0. The G + C content of the genomic DNA was 69.5%. Based on these genotypic and phenotypic data, it is supported that strain WRP15-2T represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora oryzae sp. nov. is proposed. The type strain is WRP15-2T ( = TBRC 15728T = NBRC 115560T).

Rare rhizo-Actinomycetes: A new source of agroactive metabolites

Numerous biotic and abiotic stress in some geographical regions predisposed their agricultural matrix to challenges threatening plant productivity, health, and quality. In curbing these threats, different customary agrarian principles have been created through research and development, ranging from chemical inputs and genetic modification of crops to the recently trending smart agricultural technology. But the peculiarities associated with these methods have made agriculturists rely on plant rhizospheric microbiome services, particularly bacteria. Several bacterial resources like Proteobacteria, Firmicutes, Acidobacteria, and Actinomycetes (Streptomycetes) are prominent as bioinoculants or the application of their by-products in alleviating biotic/abiotic stress have been extensively studied, with a dearth in the application of rare Actinomycetes metabolites. Rare Actinomycetes are known for their colossal genome, containing well-preserved genes coding for prolific secondary metabolites with many agroactive functionalities that can revolutionize the agricultural industry. Therefore, the imperativeness of this review to express the occurrence and distributions of rare Actinomycetes diversity, plant and soil-associated habitats, successional track in the rhizosphere under diverse stress, and their agroactive metabolite characteristics and functionalities that can remediate the challenges associated with agricultural productivity.

Saccharopolyspora soli sp. nov., isolated from Northern Cyprus soil

A novel Gram-stain positive, aerobic, non-motile actinobacterium, designated strain K220^T, was isolated from soil collected from Cape Andreas (Zafer Burnu), Northern Cyprus, and subjected to a polyphasic taxonomic approach. The organism was shown to have phylogenetic, chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Saccharopolyspora. 16S rRNA gene sequence analysis of strain K220^T showed that it is closely related to the type strains of Saccharopolyspora maritima 3SS5-12 ^T, Saccharopolyspora kobensis JCM 9109 ^T and Saccharopolyspora hirsuta ATCC 27875 ^T with 97.6, 97.5 and 97.0% sequence similarity, respectively. In silico DNA-DNA hybridization and average nucleotide identity values between strain K220^T and type strains of the genus Saccharopolyspora with publicly available genomes were 22.1-31.2% and 76.0-83.16%, respectively. The DNA G + C content of strain K220^T was 68.3 mol%. The genome of strain K220^T has genes associated with 24 biosynthetic gene clusters. The strain contained MK-9(H₄) and iso-C_16: 0 as the predominant respiratory quinone and fatty acid, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine. Based on evidence collected from the genotypic, phenotypic and phylogenetic analyses, strain K220^T is considered to represent a novel species in the genus Saccharopolyspora, for which the name Saccharopolyspora soli sp. nov. is proposed. The type strain is K220^T (= JCM 33912^T = KCTC 49395^T).