Genotype-phenotype correlations within the Geodermatophilaceae

Trujillonella humicola sp. nov., a siderophore-synthesizing bacterium isolated from black soil in Northeast China

A Gram-stain-positive, motile, and oval-shaped bacterium, designated as SYSU BS000539T, was isolated from black soil in Heilongjiang Province, China. 16S rRNA gene sequencing revealed that the isolate shared the highest similarity to Trujillonella endophytica DSM 45413T (98.32%), and phylogenetic analysis confirmed that it belonged to the genus Trujillonella. The strain could grow at temperatures from 15 to 37 °C (with an optimum at 28 °C), in salt concentrations of 0-5% (w/v) (with an optimum at 0%), and at pH levels from 6.0 to 10.0 (with an optimum at 8.0). The dominant cellular fatty acids (> 5%) were iso-C16:0, iso-C15:0, and iso-C16:1, while the principal respiratory quinones was menaquinone MK-9 (H4) with menaquinone MK-8 as minor components. Polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol methylphosphonolipid, an unidentified aminolipid and two unidentified polar lipids. The G + C content of the genome was 74.97%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SYSU BS000539T and T. endophytica DSM 45413T were 84.10% and 27.60%, respectively, falling below species delineation thresholds. Combining phylogenetic, genotypic, chemotaxonomic, physiological and biochemical analyses, it is evident that SYSU BS000539T represented a novel species within the genus Trujillonella, for which the name Trujillonella humicola sp. nov. is proposed. The type strain of the proposed novel species is SYSU BS000539T (= MCCC 1K09330T = KCTC 59402T).

Ecogenomic insights into the resilience of keystone Blastococcus Species in extreme environments: a comprehensive analysis

BACKGROUND

The stone-dwelling genus Blastococcus plays a key role in ecosystems facing extreme conditions such as drought, salinity, alkalinity, and heavy metal contamination. Despite its ecological significance, little is known about the genomic factors underpinning its adaptability and resilience in such harsh environments. This study investigates the genomic basis of Blastococcus's adaptability within its specific microniches, offering insights into its potential for biotechnological applications.

RESULTS

Comprehensive pangenome analysis revealed that Blastococcus possesses a highly dynamic genetic composition, characterized by a small core genome and a large accessory genome, indicating significant genomic plasticity. Ecogenomic assessments highlighted the genus's capabilities in substrate degradation, nutrient transport, and stress tolerance, particularly on stone surfaces and archaeological sites. The strains also exhibited plant growth-promoting traits, enhanced heavy metal resistance, and the ability to degrade environmental pollutants, positioning Blastococcus as a candidate for sustainable agriculture and bioremediation. Interestingly, no correlation was found between the ecological or plant growth-promoting traits (PGPR) of the strains and their isolation source, suggesting that these traits are not linked to their specific environments.

CONCLUSIONS

This research highlights the ecological and biotechnological potential of Blastococcus species in ecosystem health, soil fertility improvement, and stress mitigation strategies. It calls for further studies on the adaptation mechanisms of the genus, emphasizing the need to validate these findings through wet lab experiments. This study enhances our understanding of microbial ecology in extreme environments and supports the use of Blastococcus in environmental management, particularly in soil remediation and sustainable agricultural practices.

Genomic and Phenotypic Characterization of Streptomyces sirii sp. nov., Amicetin-Producing Actinobacteria Isolated from Bamboo Rhizospheric Soil

In our large-scale search for antimicrobial-producing bacteria, we isolated an actinomycete strain from rhizospheric soil of Bambusa vulgaris. The strain designated BP-8 showed noticeable antibacterial activity. BP-8 was subjected to a whole-genome analysis via a polyphasic taxonomy approach, and its antibacterial metabolite was identified by HRLS-MS. The results of the physiological and morphological analyses indicated that BP-8 is an aerobic, neutrophilic, mesophilic organism that is tolerant to 8% NaCl and can use a wide range of carbohydrates. It forms curly sporophores with a warty surface. The results of the phylogenetic and average nucleotide identity analyses and in silico DNA-DNA hybridization calculation indicated that BP-8 represents the type strain of a novel Streptomyces species. A comparative in silico analysis of the genome sequences of BP-8 and its closest related strains revealed the presence of genes encoding chemotaxonomic markers characteristic of Streptomyces. The antibacterial compound was identified as amicetin. Genomic mining also revealed more than 10 biosynthetic gene clusters that have not been described previously and may lead to the discovery of new valuable compounds. On the basis of these results, strain BP-8T (=VKM Ac-3066T = CCTCC AA 2024094T) is proposed as the type strain of the novel species Streptomyces sirii sp. nov.

Geodermatophilus maliterrae sp. nov., a member of the Geodermatophilaceae isolated from badland surfaces in the Red Desert, Wyoming, USA

A novel Gram-stain-positive, black-pigmented bacterium, designated as WL48A T, was isolated from the surface of badland sedimentary rock in the Red Desert of Wyoming and characterized using a polyphasic taxonomic approach. Good growth occurred at 28-32 °C, pH 7-9, and NaCl less than 1% (w/v). Colonies, growing well on International Streptomyces Project media (ISP) 3 and ISP 7, were black and adhering to the agar. Phylogenetic analyses based on 16S rRNA gene and draft genome sequences showed that strain WL48AT belongs to the family Geodermatophilaceae, forming a distinct sub-branch with Geodermatophilus bullaregiensis DSM 46841T. The organism showed 16S rRNA gene sequence similarity of 98.8% with G. bullaregiensis DSM 46841T. Digital DNA-DNA hybridization value between the genome sequences of strain WL48A T and G. bullaregiensis DSM 46841T was 51.8%, below the threshold of 70% for prokaryotic species delineation. The chemotaxonomic investigation revealed the presence of galactose, glucose, mannose, xylose and ribose as well as meso-DAP in the peptidoglycan layer. The polar lipid profiles contained phosphatidylcholine (PC), phosphatidylinositol (PI), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE) phosphoglycolipid, phospholipids and an unidentified lipid. The menaquinone profile consisted of MK-9(H4) (98.2%) and MK-9(H2) (10.8%). The major fatty acid profile (>15%) comprised iso-C15 : 0 and iso-C16 : 0. Based on phenotypic, genetic and genomic data, strain WL48AT (=DSM 116197T = NCIMB 15483T=NCCB 100957T =ATCC TSD-376T) merits to be considered as a novel species for which the name Geodermatophilus maliterrae sp. nov. is proposed.

Blastococcus montanus sp. nov., a multi-stress-resistant and bacteriostatic-producing bacterium isolated from the Flaming Mountain, Xinjiang,China

A bacterial strain designated HT6-4T was isolated from soil samples collected from the Flaming Mountain, Xinjiang, PR China. The purpose of this study was to describe a novel species and its characteristics, through genome sequencing and analysis of the relationship between the members of the genus Blastococcus, and explore the antiradiation, antioxidation and antibacterial capabilities of strain HT6-4T. The polyphasic study confirmed the affiliation of strain HT6-4T with the genus Blastococcus. Strain HT6-4T was aerobic, Gram-stain-positive, non-budding, non-motile, catalase-positive and oxidase-negative. It grew at 10-37 °C, pH 5.0-8.0 and 0-4% (w/v) NaCl. Colonies were circular, smooth and bright orange in colour. In addition, strain HT6-4T was drought tolerant. The predominant menaquinone was MK-9, with MK-8 as the minor component. The polar lipids of strain HT6-4T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, phospholipids, an unidentified aminolipid and two unidentified phospholipids. Whole-cell hydrolysates contain meso-diaminopimelic acid as the diagnostic diamino acid and ribose and galactose as diagnostic sugars. Its major fatty acids were iso-C16 :  0, C17 :  1 ω8c and C18 :  1 ω9c. The genome of strain HT6-4T was 4.30 Mb in the whole-genome shotgun project. The G+C content was 73.9 mol%. The phylogenetic analysis based on the 16S rRNA gene sequence showed that strain HT6-4T was closely related to Blastococcus jejuensis KST3-10T(97.9%), Blastococcus capsensis BMG 804T(97.8%), Blastococcus aggregatus DSM 4725T(97.5%), Blastococcus saxobsidens BC 444T(97.5%), Blastococcus xanthinilyticus BMG 862T(97.5%) and Blastococcus litoris GP-S2-8T(97.5%). The average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) values among strain HT6-4T and B. jejuensis KST3-10T, B. capsensis BMG 804T, B. aggregatus DSM 4725T, B. saxobsidens BC 444T, B. xanthinilyticus BMG 862T and B. litoris GP-S2-8T were below the species delimitation thresholds. The genome of strain HT6-4T contained antiradiation genes, antioxidant genes and antibacterial genes. Based on its morphological, physiological and chemical taxonomic characteristics, strain HT6-4T (=KCTC 59234T =GDMCC 1.4386T) should be classified as a novel species of the genus Blastococcus with the proposed name Blastococcus montanus sp. nov.

Biotechnological and pharmaceutical potential of twenty-eight novel type strains of Actinomycetes from different environments worldwide

Actinomycetes are a prolific source of bioactive natural compounds many of which are used as antibiotics or other drugs. In this study we investigated the genomic and biochemical diversity of 32 actinobacterial strains that had been deposited at the DSMZ-German Collection of Microorganisms and Cell Cultures decades ago. Genome-based phylogeny and in silico DNA-DNA hybridization supported the assignment of these strains to 26 novel species and two novel subspecies and a reclassification of a Streptomyces species. These results were consistent with the biochemical, enzymatic, and chemotaxonomic features of the strains. Most of the strains showed antimicrobial activities against a range of Gram-positive and Gram-negative bacteria, and against yeast. Genomic analysis revealed the presence of numerous unique biosynthetic gene clusters (BGCs) encoding for potential novel antibiotic and anti-cancer compounds. Strains DSM 41636T and DSM 61640T produced the antibiotic compounds A33853 and SF2768, respectively. Overall, this reflects the significant pharmaceutical and biotechnological potential of the proposed novel type strains and underlines the role of prokaryotic systematics for drug discovery. In order to compensate for the gender gap in naming prokaryotic species, we propose the eponyms for all newly described species to honour female scientists.

Proposal for reclassification of the species Hungatella xylanolytica as Lacrimispora xylanisolvens nom. nov. and transfer of the genus Hungatella to the family Lachnospiraceae

Hungatella xylanolytica X5-1T is an anaerobic, xylan-fermenting bacterium first isolated from methane-producing cattle manure. Initially identified as Bacteroides xylanolyticus, this species was later reclassified as H. xylanolytica in 2019. Although this reclassification found support through Genome blast Distance Phylogeny analysis which placed H. xylanolytica X5-1T into the same clade as Hungatella effluvii DSM 24995T, it was contradicted by 16S rRNA gene phylogenetic analysis, which associated it with a set of misnamed Clostridium species later reassigned into the genus Lacrimispora. To ascertain its taxonomic position, comparative analyses were performed to re-examine the relationship between H. xylanolytica X5-1T and all species of the genera Hungatella and Lacrimispora. The ranges of 16S rRNA gene sequence similarity, average amino acid identity, and percentage of conserved protein prediction values were higher between H. xylanolytica X5-1T and species of the genus Lacrimispora than Hungatella. In addition, H. xylanolytica X5-1T was found to harbour genes and pathways conserved and exclusive to species within the genus Lacrimispora but not Hungatella. Essentially, in both the 16S rRNA gene phylogenetic tree and the core-genome phylogenomic tree, H. xylanolytica X5-1T clustered into the same clade as species of the genus Lacrimispora, distinct from species of the genus Hungatella. It is thus clear that H. xylanolytica X5-1T represents a species within the genus Lacrimispora, which we propose to reclassify as Lacrimispora xylanisolvens nom. nov. Finally, based on the results from the phylogenetic and comparative analyses, the genus Hungatella was transferred to the family Lachnospiraceae.

Blastococcus brunescens sp. nov., a member of the Geodermatophilaceae isolated from sandstone collected from the Sahara Desert in Tunisia

The taxonomic position of strain BMG 8361T, isolated from sandstone collected in the Sahara Desert of Southern Tunisia, was refined through a polyphasic taxonomic investigation. Colonies of BMG 8361T were pale-orange coloured, irregular with a dry surface and produced a diffusible pink or brown pigment depending on media. The Gram-positive cells were catalase-positive and oxidase-negative. The strain exhibited growth at 10-40 °C and pH values ranging from 5.5 to 9.0, with optima at 28-35 °C and pH 6.5-8.0. Additionally, BMG 8361T demonstrated the ability to grow in the presence of up to 1 % NaCl (w/v) concentration. The peptidoglycan of the cell wall contained meso-diaminopimelic acid, glucose, galactose, xylose, ribose, and rhamnose. The predominant menaquinones consisted of MK-9(H4) and MK-9. The main polar lipids were phosphatidylcholine, phosphatidylinositol, glycophosphatidylinositol, diphosphatidylglycerol, phosphatidylethanolamine, and two unidentified lipids. Major cellular fatty acids were iso-C16 : 0, iso-C16 : 1 h, and C17 : 1  ω8c. Phylogenetic analyses based on both the 16S rRNA gene and whole-genome sequences assigned strain BMG 8361T within the genus Blastococcus. The highest pairwise sequence similarity observed in the 16S rRNA gene was 99.5 % with Blastococcus haudaquaticus AT 7-14T. However, when considering digital DNA-DNA hybridization and average nucleotide identity, the highest values, 48.4 and 86.58 %, respectively, were obtained with Blastococcus colisei BMG 822T. These values significantly undershoot the recommended thresholds for establishing new species, corroborating the robust support for the distinctive taxonomic status of strain BMG 8361T within the genus Blastococcus. In conjunction with the phenotyping results, this compelling evidence leads to the proposal of a novel species we named Blastococcus brunescens sp. nov. with BMG 8361T (=DSM 46845T=CECT 8880T) as the type strain.

Lactiplantibacillus brownii sp. nov., a novel psychrotolerant species isolated from sauerkraut

A Gram-stain-positive, rod-shaped, facultatively anaerobic and homofermentative strain, named WILCCON 0030T, was isolated from sauerkraut (fermented cabbage) collected from a local market in the Moscow region of Russia. Comparative analyses based on 16S rRNA gene sequence similarity and whole genome relatedness indicated that strain WILCCON 0030T was most closely related to the type strains Lactiplantibacillus nangangensis NCIMB 15186T, Lactiplantibacillus daoliensis LMG 31171T and Lactiplantibacillus pingfangensis LMG 31176T. However, the average nucleotide identity and digital DNA-DNA hybridization prediction values with these closest relatives only ranged from 84.6 to 84.9 % and from 24.1 to 24.7 %, respectively, and were below the 95.0 and 70.0% thresholds for species delineation. Substantiated by further physiological and biochemical analyses, strain WILCCON 0030T represents a novel species within the genus Lactiplantibacillus for which we propose the name Lactiplantibacillus brownii sp. nov. (type strain WILCCON 0030T=DSM 116485T=LMG 33211T).

Blastococcus carthaginiensis sp. nov., isolated from a monument sampled in Carthage, Tunisia

A comprehensive polyphasic investigation was conducted to elucidate the taxonomic position of an actinobacterium, designated BMG 814T, which was isolated from the historic ruins of Carthage city in Tunisia. It grew as pink-orange pigmented colonies and displayed versatile growth capabilities, thriving within a temperature range of 20-40 °C, across a pH spectrum ranging from pH 5.5 to 10 and in the presence of up to 4 % NaCl. Chemotaxonomic investigations unveiled specific cell components, including diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, an unidentified aminoglycophospholipid, six unidentified aminolipids, two unidentified phospholipids and one unidentified lipid in its polar lipid profile. Furthermore, galactose, glucose and ribose were identified as the primary cell-wall sugars. Major menaquinones identified were MK-9(H4), MK-9(H2) and MK-9, while major fatty acids comprised iso-C15 : 0, iso-C16 : 0, C17 : 1  ω8c and C18 : 1  ω9c. Through phylogenetic analysis based on the 16S rRNA gene sequence, the strain was positioned within the genus Blastococcus, with Blastococcus capsiensis BMG 804T showing the closest relationship (99.1 %). In light of this, draft genomes for both strains, BMG 814T and BMG 804T, were sequenced in this study, and comparative analysis revealed that strain BMG 814T exhibited digital DNA-DNA hybridization and average nucleotide identity values below the recommended thresholds for demarcating new species with all available genomes of type strains of validly names species. Based on the polyphasic taxonomy assessment, strain BMG 814T (=DSM 46848T=CECT 8878T) was proposed as the type strain of a novel species named Blastococcus carthaginiensis sp. nov.