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This study aims to evaluate the in silico genomic characteristics of five species of the genus Planotetraspora : P. kaengkrachanensis , P. mira , P. phitsanulokensis , P. silvatica , and P. thailandica , with a view to their application in therapeutic research. The 16S rRNA comparison indicated that these species were phylogenetically distinct. Pairwise comparisons of digital DNA-DNA hybridization (dDDH) and OrthoANI values between these studied type strains indicated that dDDH values were below 62.5%, while OrthoANI values were lower than 95.3%, suggesting that the five species represent distinct genomospecies. These results were consistent with the phylogenomic study based on core genes and the pangenome analysis of these five species within the genus Planotetraspora . However, the genome annotation showed some differences between these species, such as variations in the number of subsystem category distributions across whole genomes (ranging between 1979 and 2024). Additionally, the number of CAZYme (Carbohydrate-Active enZYme) genes ranged between 298 and 325, highlighting the potential of these bacteria for therapeutic research applications. The in silico physico-chemical characteristics of cellulases from Planotetraspora species were analyzed. Their 3D structure was modeled, refined, and validated. A molecular docking analysis of this cellulase protein structural model was conducted with cellobiose, cellotetraose, laminaribiose, carboxymethyl cellulose, glucose, and xylose ligand. Our study revealed significant interaction between the Planotetraspora cellulase and cellotetraose substrate, evidenced by stable binding energies. This suggests that this bacterial enzyme holds great potential for utilizing cellotetraose as a substrate in various applications. This study enriches our understanding of the potential applications of Planotetraspora species in therapeutic research.

A comprehensive polyphasic taxonomic investigation integrating taxongenomic criteria was conducted on strain IRAMC:0171 T isolated from the root nodules of Retama raetam in Tunisia. This Gram-stain-negative and aerobic bacterium thrived within a temperature range of 5-45 °C, optimal at 28 °C, and tolerated salt concentrations from 0-6 % NaCl, with an optimal range of 0-3 %. It displayed pH tolerance from pH 4 to 10, thriving best at pH 6.8-7.5. Chemotaxonomically, strain IRAMC:0171 T was characterized by diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and phosphatidylethanolamine as polar lipids. Its predominant fatty acid composition was C 18 : 1  ω 7c (61.2 %), and the primary ubiquinone was Q10 (97 %). Analysis of the 16S rRNA gene of strain IRAMC:0171 T showed 99.08 % similarity to Mesorhizobium waimense ICMP 19557 T , Mesorhizobium amorphae ACCC 19665 T , and Mesorhizobium huakuii IAM 14158. However, digital DNA-DNA hybridization and average nucleotide identity analyses revealed values ranging from 21.1 to 25.2 % and 77.05 to 82.24 %, respectively, signifying significant deviation from established species demarcation thresholds. Phylogenetic studies, encompassing 16S rRNA, whole-genome-based tree reconstruction, and core protein analysis, positioned strain IRAMC:0171 T closest to Mesorhizobium terrae KCTC 72278 T and ' Mesorhizobium hungaricum ' UASWS1009 T , forming together a distinct branch within the genus Mesorhizobium . In consideration of this comprehensive data, we propose strain IRAMC:0171 T (=DSM 112841 T =CECT 30767 T ) as the type strain of a new species named Mesorhizobium retamae sp. nov.

Streptomyces sp. DSM 41014, DSM 41527, and DSM 41981 are three strains from the DSMZ strain collection. Here, we present the draft genome sequences of DSM 41014, DSM 41527, and DSM 41981 with a size of 9.09 Mb, 8.45 Mb, and 9.23 Mb, respectively., Competing Interests: The authors declare that there are no conflicts of interest., (Copyright © 2024 The Authors.)

The taxonomic position of three actinobacterial strains, BCCO 10&#95;0061 T , BCCO 10&#95;0798 T , and BCCO 10&#95;0856 T , recovered from bare soil in the Sokolov Coal Basin, Czech Republic, was established using a polyphasic approach. The multilocus sequence analysis based on 100 single-copy genes positioned BCCO 10&#95;0061 T in the same cluster as Lentzea waywayandensis , strain BCCO 10&#95;0798 T in the same cluster as Lentzea flaviverrucosa , Lentzea californiensis , Lentzea violacea , and Lentzea albidocapillata , and strain BCCO 10&#95;0856 T clustered together with Lentzea kentuckyensis and Lentzea alba . Morphological and chemotaxonomic characteristics of these strains support their assignment to the genus Lentzea . In all three strains, MK-9(H 4 ) accounted for more than 80 % of the isoprenoid quinone. The diagnostic diamino acid in the cell-wall peptidoglycan was meso -diaminopimelic acid. The whole-cell sugars were rhamnose, ribose, mannose, glucose, and galactose. The major fatty acids (>10 %) were iso-C 15 : 0 , anteiso-C 15 : 0 , iso-C 16 : 0 , and C 16 : 0 . The polar lipids were diphosphatidylglycerol, methyl-phosphatidylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol. The genomic DNA G+C content of strains (mol%) was 68.8 for BCCO 10&#95;0061 T , 69.2 for BCCO 10&#95;0798 T , and 68.5 for BCCO 10&#95;0856 T . The combination of digital DNA-DNA hybridization results, average nucleotide identity values and phenotypic characteristics of BCCO 10&#95;0061 T , BCCO 10&#95;0798 T , and BCCO 10&#95;0856 T distinguishes them from their closely related strains. Bioinformatic analysis of the genome sequences of the strains revealed several biosynthetic gene clusters (BGCs) with identities >50 % to already known clusters, including BGCs for geosmin, coelichelin, ε-poly-l-lysine, and erythromycin-like BGCs. Most of the identified BGCs showed low similarity to known BGCs (<50 %) suggesting their genetic potential for the biosynthesis of novel secondary metabolites. Based on the above results, each strain represents a novel species of the genus Lentzea , for which we propose the name Lentzea sokolovensis sp. nov. for BCCO 10&#95;0061 T (=DSM 116175 T ), Lentzea kristufekii sp. nov. for BCCO 10&#95;0798 T (=DSM 116176 T ), and Lentzea miocenica sp. nov. for BCCO 10&#95;0856 T (=DSM 116177 T ).

The Gram-positive bacteria Streptomyces davaonensis and Streptomyces cinnabarinus have been the only organisms known to produce roseoflavin, a riboflavin (vitamin B 2 ) derived red antibiotic. Using a selective growth medium and a phenotypic screening, we were able to isolate a novel roseoflavin producer from a German soil sample. The isolation procedure was repeated twice, that is, the same strain could be isolated from the same location in Berlin 6 months and 12 months after its first isolation. Whole genome sequencing of the novel roseoflavin producer revealed an unusual chromosomal arrangement and the deposited genome sequence of the new isolate (G + C content of 71.47%) contains 897 genes per inverted terminal repeat, 6190 genes in the core and 107 genes located on an illegitimate terminal end. We identified the roseoflavin biosynthetic genes rosA, rosB and rosC and an unusually high number of riboflavin biosynthetic genes. Overexpression of rosA, rosB and rosC in Escherichia coli and enzyme assays confirmed their predicted functions in roseoflavin biosynthesis. A full taxonomic analysis revealed that the isolate represents a previously unknown Streptomyces species and we propose the name Streptomyces berlinensis sp. nov. for this roseoflavin producer., (© 2024 The Authors. Environmental Microbiology Reports published by John Wiley & Sons Ltd.)

Strain collections are a treasure chest of numerous valuable and taxonomically validated bioresources. The Leibniz Institute DSMZ is one of the largest and most diverse microbial strain collections worldwide, with a long tradition of actinomycetes research. Actinomycetes, especially the genus Streptomyces , are renowned as prolific producers of antibiotics and many other bioactive natural products. In light of this, five Streptomyces strains, DSM 40971 T , DSM 40484 T , DSM 40713 T , DSM 40976 T , and DSM 40907 T , which had been deposited a long time ago without comprehensive characterization, were the subject of polyphasic taxonomic studies and genome mining for natural compounds based on in vitro and in silico analyses. Phenotypic, genetic, and phylogenomic studies distinguished the strains from their closely related neighbors. The digital DNA-DNA hybridization and average nucleotide identity values between the five strains and their close, validly named species were below the threshold of 70% and 95%-96%, respectively, determined for prokaryotic species demarcation. Therefore, the five strains merit being considered as novel Streptomyces species, for which the names Streptomyces kutzneri sp. nov., Streptomyces stackebrandtii sp. nov. , Streptomyces zähneri sp. nov. , Streptomyces winkii sp. nov., and Streptomyces kroppenstedtii sp. nov. are proposed. Bioinformatics analysis of the genome sequences of the five strains revealed their genetic potential for the production of secondary metabolites, which helped identify the natural compounds cinerubin B from strain DSM 40484 T and the phosphonate antibiotic phosphonoalamide from strain DSM 40907 T and highlighted strain DSM 40976 T as a candidate for regulator-guided gene cluster activation due to the abundance of numerous " Streptomyces antibiotic regulatory protein" (SARP) genes., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Nouioui, Zimmermann, Hennrich, Xia, Rössler, Makitrynskyy, Pablo Gomez-Escribano, Pötter, Jando, Döppner, Wolf, Neumann-Schaal, Hughes and Mast.)

Streptomyces Strain San01 is isolated from the soil of ant-nest found in the tea estate of Darjeeling, India. The morphology, biochemical, as well as the molecular characteristics, proved that San01 belonged to the genus Streptomyces. The average nucleotide identity (ANI) value between the genome sequence of the studied strain and its closest phylogenetic neighbors were very low and also could be distinguished from its closest neighbour with broad range of phenotypic data. The draft genome sequence of isolate San01 (NZ&#95;RZYA00000000.1) was estimated to be 9.12 Mbp in size with 71.2% of GC content and it encompasses 39 biosynthetic gene clusters that emphasize the biotechnological potential of this isolate . Based on the phenotypic, genetic and genomic data, isolate San01 (=JCM 34633 = NCTC 14543) merits to be recognized as a type strain of a novel species and hereby propose the name Streptomyces antnestii sp. nov. Incidentally, this is the first report on Streptomyces genomes from Darjeeling, India., Competing Interests: Competing Interests: The authors have declared that no competing interest exists., (© The author(s).)

Strains CN4 T , CN6, CN7 and CNm7 were isolated from root nodules of Coriaria nepalensis from Murree in Pakistan. They do not form root nodules on C. nepalensis nor on Alnus glutinosa although they deformed root hairs of Alnus . The colonies are bright red-pigmented, the strains form hyphae and sporangia but no N 2 -fixing vesicles and do not fix nitrogen in vitro . The peptidoglycan of strain CN4 T contains meso -diaminopimelic acid; whole cell sugars consist of ribose, mannose, glucose, galactose and rhamnose. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unknown lipids represent the major polar lipids; MK-9(H 4 ) and MK-9(H 6 ) are the predominant menaquinones (>15 %), and iso-C 16 : 0 and C 17 : 1 ω8 c are the major fatty acids (>15 %). The results of comparative 16S rRNA gene sequence analyses indicated that strain CN4 T is most closely related to Frankia saprophytica CN 3 T . An MLSA phylogeny using amino acids sequences of AtpD, DnaA, FtsZ, Pgk and RpoB, assigned the strain to cluster 4 non-nodulating species, close to F. saprophytica CN 3 T , Frankia asymbiotica M16386 T and Frankia inefficax EuI1c T with 0.04 substitutions per site, while that value was 0.075 with other strains. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between CN4 T and all species of the genus Frankia with validly published names were below the defined threshold for prokaryotic species demarcation, with dDDH and ANI values at or below 27.8 and 83.7 %, respectively. The four strains CN4 T , CN6, CN7 and CNm7 had dDDH (98.6-99.6 %) and ANI values that grouped them as representing a single species. CN4 T has a 10.76 Mb genome. CN4 T was different from its close phylogenetic neighbours with validly published names in being red-pigmented, in having several lantibiotic-coding clusters, a carbon monoxide dehydrogenase cluster and a clustered regularly interspaced short palindromic repeats (CRISPR) cluster. The results of phenotypic, physiological and phylogenomic analyses confirmed the assignment of strain CN4 T (=DSM 114740 T = LMG 32595 T ) to a novel species, with CN4 T as type strain, for which the name Frankia nepalensis sp. nov. is proposed.

Two novel Micromonospora strains, STR1-7 T and STR1S-6 T , were isolated from the rhizosphere of a Parastrephia quadrangularis plant growing in the Salar de Tara region of the Atacama Desert, Chile. Chemotaxonomic, cultural and phenotypic features confirmed that the isolates belonged to the genus Micromonospora . They grew from 20 to 37 °C, from pH7 to 8 and in the presence of up to 3 %, w/v NaCl. The isolates formed distinct branches in Micromonospora gene trees based on 16S rRNA gene sequences and on a multi-locus sequence analysis of conserved house-keeping genes. A phylogenomic tree generated from the draft genomes of the isolates and their closest phylogenetic neighbours showed that isolate STR1-7 T is most closely related to Micromonospora orduensis S2509 T , and isolate STR1S-6 T forms a distinct branch that is most closely related to 12 validly named Micromonospora species, including Micromonospora saelicesensis the earliest proposed member of the group. The isolates were separated from one another and from their closest phylogenomic neighbours using a combination of chemotaxonomic, genomic and phenotypic features, and by low average nucleotide index and digital DNA-DNA hybridization values. Consequently, it is proposed that isolates STR1-7 T and STR1S-6 T be recognized as representing new species in the genus Micromonospora , namely as Micromonospora parastrephiae sp. nov. and Micromonospora tarensis sp. nov.; the type strains are STR1-7 T (=CECT 9665 T =LMG 30768 T ) and STR1S-6 T (=CECT 9666 T =LMG 30770 T ), respectively. Genome mining showed that the isolates have the capacity to produce novel specialized metabolites, notably antibiotics and compounds that promote plant growth, as well as a broad-range of stress-related genes that provide an insight into how they cope with harsh abiotic conditions that prevail in high-altitude Atacama Desert soils.

Strain TÜ4103 T was originally sampled from Java, Indonesia and deposited in the Tübingen strain collection under the name ' Streptomyces sp.'. The strain was found to be an antibiotic producer as strain TÜ4103 T showed bioactivity against Gram-positive bacteria, such as Bacillus subtilis and Kocuria rhizophila in bioassays. Strain TÜ4103 T showed 16S rRNA gene sequence similarity of 99.65 % to Kitasatospora cheerisanensis DSM 101999 T and 98.82 % to Kitasatospora niigatensis DSM 44781 T and Kitasatospora cineracea DSM 44780 T . Genome-based phylogenetic analysis revealed that strain TÜ4103 T is closely related to K. cineracea DSM 44780 T and K. niigatensis DSM 44781 T . The digital DNA-DNA hybridization values between the genome sequences of strain TÜ4103 T and its closest phylogenomic relatives, strains DSM 44780 T and DSM 44781 T , were 43.0 and 42.9 %, respectively. Average nucleotide identity (ANI) values support this claim, with the highest ANI score of 91.14 % between TÜ4103 T and K. niigatensis being closely followed by an ANI value of 91.10 % between K. cineracea and TÜ4103 T . The genome of TÜ4103 T has a size of 7.91 Mb with a G+C content of 74.05 mol%. Whole-cell hydrolysates of strain TÜ4103 T are rich in meso -diaminopimelic acid, and rhamnose, galactose and mannose are characteristic as whole-cell sugars. The phospholipid profile contains phosphatidylethanolamine, diphosphatidylglycerol and glycophospholipid. The predominant menaquinones (>93.5 %) are MK-9(H 8 ) and MK-9(H 6 ). Based on the phenotypic, genotypic and genomic characteristics, strain TÜ4103 T (=DSM 114396 T =CECT 30712 T ) merits recognition as the type strain of a novel species of the genus Kitasatospora , for which the name Kitasatospora fiedleri sp. nov. is proposed.

Strains USC-21046 T and USC-21048 T were isolated from foaming coastal marine waters on the Sunshine Coast, Queensland, Australia. Both strains displayed growth and morphological characteristics typical for members belonging to the genus Nocardia . The major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine, and the major fatty acids were C 16 : 0 , C 18 : 1  ω9 c , C 18 : 0 and C 18 : 0 10-methyl. The mycolic acids of strains USC-21046 T and USC-21048 T consisted of chain lengths between 50-64 and 56-68, respectively. Moreover, both of those strains contained meso -diaminopimelic acid and ribose, arabinose, glucose and galactose as whole cell sugars. Based on the phylogenomic results, both strains belonged to the genus Nocardia with strain USC-21046 T showing an 80.4 % genome similarity to N. vinacea NBRC 16497 T and N. pseudovaccinii NBRC 100343 T , whereas USC-21048 T strain showed an 83.6 % genome similarity to N. aobensis NBRC 100429 T . Both strains were delineated from their closely related relatives based on physiological (e.g. growth on sole carbon source) and chemotaxonomic (e.g. cellular fatty composition) differences. The digital DNA-DNA hybridization (dDDH) values between USC-21046 T and USC-21048 T and their closely related relatives were below the dDDH threshold value of ≤70 % used for the taxonomic classification of novel species status. The genome length of strains USC-21046 T and USC-21048 T were 6 878 863 and 7 066 978 bp, with G+C contents of 65.2 and 67.8 mol%, respectively. For the novel isolates, we propose the names Nocardia australiensis sp. nov. with the type strain USC-21046 T (=DSM 111727 T =NCCB 100867 T ) and Nocardia spumae sp. nov. with the type strain USC-21048 T (=DSM 111726 T =NCCB 100868 T ).

Frankia strain Ag45/Mut15 T was isolated from a root nodule of Alnus glutinosa growing in a swamp at lake Grossensee, Germany. The strain forms root nodules on A. glutinosa , in which it produces hyphae and clusters of N 2 -fixing vesicles. N 2 -fixing vesicles are also produced in nitrogen-free growth medium, in addition to hyphae and sporangia. The whole-cell hydrolysates of strain Ag45/Mut15 T contained meso -diaminopimelic acid in the peptidoglycan and ribose, xylose, mannose, glucose, galactose and a trace of rhamnose as cell-wall sugars. The major polar lipids were phosphatidylglycerol, phosphatidylinositol, diphosphatidylglycerol and glyco-phospholipid. The predominant (>20 %) menaquinones were MK-9(H 6 ) and MK-9(H 4 ). The major fatty acid profile (>10 %) consisted of iso-C 16:0 , C 17 : 1  ω8 c and C 17 : 0 . Pairwise 16S rRNA gene distances showed that strain Ag45/Mut15 T was most closely related to Frankia torreyi CpI1 T and Candidatus Frankia nodulisporulans with 16S rRNA gene similarity values of 0.001335 substitutions per site. An multilocus sequence analysis phylogeny based on atpD , dnaA , ftsZ , pgk and rpoB amino acid sequences positioned the strain within cluster 1 of Alnus - and Myrica -nodulating species, close to Candidatus F. nodulisporulans AgTrS T and F. canadensis ARgP5 T . The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the studied strain Ag45/Mut15 T and all validly named Frankia species were below the defined threshold for prokaryotic species demarcation. Candidatus F. nodulisporulans AgTrS T , which cannot be cultivated in vitro , was found to be the closest phylogenetic neighbour to strain strain Ag45/Mut15 T with dDDH and ANI values of 61.8 and 97 %, respectively. Strain Ag45/Mut15 T was not able to sporulate in nodule tissues like strain AgTrS T .Phenotypic, physiological and phylogenomic analyses confirmed the assignment of strain Ag45/Mut15 T (=DSM 114737 T =LMG 326O1 T ) to a novel species, with Ag45/Mut15 T as type strain, for which the name Frankia umida sp. nov. is proposed.

A nitrogen-fixing actinobacterium strain (Cc1.17 T ) isolated from a root nodule of Colletia cruciata was subjected to polyphasic taxonomic studies. The strain was characterized by the presence of meso -diaminopimelic acid in its peptidoglycan, galactose, glucose, mannose, rhamnose, ribose and xylose as cell-wall sugars, phosphatidylinositol, diphosphatidylglycerol, glycophospholipids, phosphatidylglycerol, glycophospholipid and uncharacterized lipids as its polar lipids, and C 16 : 0 , iso - C 16 : 0 , C 17 : 1 ω9 and C 18 : 1 ω 9 as major fatty acids (>10 %). Strain Cc1.17 T showed 16S rRNA gene sequence similarities of 97.4-99.8 % to validly named Frankia species. Phylogenetic trees based on 16S rRNA gene and genome sequences placed strain Cc1.17 T in a new lineage within the genus Frankia . Digital DNA-DNA hybridization and average nucleotide identity values between strain Cc1.17 T and its closest phylogenomic neighbours were well below the thresholds recommended for prokaryotic species delineation. Therefore, strain Cc1.17 T (=DSM 43829 T =CECT 9313 T ) merits recognition as the type strain of a new species for which the name Frankia colletiae sp. nov. is proposed.

Novel Corynebacterium strains, 3B T and 7B T , were isolated from the oral cavities of young chicks of yellow-eyed penguins (hoiho), Megadyptes antipodes . A polyphasic taxonomic characterization of these strains revealed chemotaxonomic, biochemical and morphological features that are consistent with those of the genus Corynebacterium . The 16S rRNA gene sequence similarity values between the strains and their closest phylogenetic neighbour, Corynebacterium ciconiae CCUG 47525 T were 99.07 %, values that are in line with their phylogenomic positions within the evolutionary radiation of the genus Corynebacterium . Digital DNA-DNA hybridization values and average nucleotide identities between the genome sequences of the two strains and related Corynebacterium species were well below the defined threshold values (70 and 95-96 %, respectively) for prokaryotic species delineation. The genome size of these strains varied between 2.45-2.46 Mb with G+C content 62.7-62.9 mol%. Strains 3B T and 7B T were Gram-stain positive bacilli that were able to grow in presence of 0-10 % (w/v) NaCl and at temperature ranging between 20-37 °C. The major fatty acids (>15 %) were C 16 : 0 and C 18 : 1  ω 9 c , and the mycolic acid profile included 32-36 carbon atoms. We propose that these strains represent a novel species, Corynebacterium megadyptis sp. nov. with 3B T (=DSM 111184 T =NZRM 4755 T ) as the type strain. Phylogenomically, strains 3B T and 7B T belong to two lineages with subtle differences in MALDI-TOF spectra, chemotaxonomic profiles and phenotypic properties. The fatty acid profile of strain 3B T contains C 18 : 0 as a predominant type (>15 %), which is a minor component in strain 7B T . Strain 7B T can oxidize N -acetyl-d-glucosamine, l-serine, α-hydroxy-butyric acid, l-malic acid, l-glutamic acid, bromo-succinic acid and l-lactic acid, characteristics not observed in strain 3B T . Therefore, we propose that these strains represent two subspecies, namely Corynebacterium megadyptis subsp. megadyptis subsp. nov. (type strain, 3B T =DSM 111184 T =NZRM 4755 T ) and Corynebacterium megadyptis subsp. dunedinense subsp. nov. (type strain, 7B T =DSM 111183 T =NZRM 4756 T ).

The status of four Frankia strains isolated from a root nodule of Alnus glutinosa was established in a polyphasic study. Taxogenomics and phenotypic features show that the isolates belong to the genus Frankia. All four strains form extensively branched substrate mycelia, multilocular sporangia, vesicles, lack aerial hyphae, but contain meso-diaminopimelic acid as the diamino acid of the peptidoglycan, galactose, glucose, mannose, ribose, xylose and traces of rhamnose as cell wall sugars, iso-C 16:0 as the predominant fatty acid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol as the major polar lipids, have comparable genome sizes to other cluster 1, Alnus-infective strains with structural and accessory genes associated with nitrogen fixation. The genome sizes of the isolates range from 7.0 to 7.7 Mbp and the digital DNA G + C contents from 71.3 to 71.5 %. The four sequenced genomes are rich in biosynthetic gene clusters predicted to express for novel specialized metabolites, notably antibiotics. 16S rRNA gene and whole genome sequence analyses show that the isolates fall into two lineages that are closely related to the type strains of Frankia alni and Frankia torreyi. All of these taxa are separated by combinations of phenotypic properties and by digital DNA:DNA hybridization scores which indicate that they belong to different genomic species. Based on these results, it is proposed that isolates Agncl-4 T and Agncl-10, and Agncl-8 T and Agncl-18, be recognised as Frankia gtarii sp. nov. and Frankia tisai sp. nov. respectively, with isolates Agncl-4 T (=DSM 107976 T  = CECT 9711 T ) and Agncl-8 T (=DSM 107980 T  = CECT 9715 T ) as the respective type strains., (Crown Copyright © 2022. Published by Elsevier GmbH. All rights reserved.)

Prokaryotic systematics is one of the most progressive disciplines that has embraced technological advances over the last century. The availability and affordability of new sequencing technologies and user-friendly software have revolutionised the discovery of novel prokaryotic taxa, including the identification and nomenclature of uncultivable microorganisms. These advances have enabled scientists to resolve the structure of complex heterogenous taxon and to rectify taxonomic status of misclassified strains due to errors associated with the sensitivity and/or reproducibility of phenotypic approaches. Time- and labour-intensive experimental characterisation of strains could be replaced with determining the presence or absence of genes or operons responsible for phenotypic and chemotaxonomic properties, such as the presence of mycolic acids and menaquinones. However, the quality of genomic data must be acceptable and phylogenomic threshold values for interspecies and supraspecies delineation should be carefully considered in combination of genome-based phylogeny for a reliable and robust classification. These technological developments have empowered prokaryotic systematists to reliably identify novel taxa with an understanding of community ecology and their biosynthetic and biodegradation potentials., (© 2022 The Authors.)

A polyphasic study was designed to resolve the taxonomic position of isolate MGRD01-02 T which was recovered from an acidic hot spring in Indonesia and assigned to the genus Actinospica. Phylogenetic analyses based on 16S rRNA gene sequences show that the isolate is most closely related to the type strains of Actinospica acidiphila (98.5%), Actinospica robiniae (97.8%) and Actinospica durhamensis (96.8%). Morphological and chemotaxonomic data underpin the assignment of the isolate to the genus Actinospica as it forms an extensively branched substrate mycelium which carries tufts of white aerial hyphae that differentiate into straight to flexuous chains of cylindrical spores with faint rugose surfaces, contains 2,6-diamino-3-hydroxydiaminopimelic acid in the peptidoglycan, mixtures of hydrogenated menaquinones with nine isoprene units, iso-C  15:O and iso-C  16:O as major fatty acids and phosphatidylethanolamine as the diagnostic phospholipid. Whole-genome sequence analyses show that the isolate, A. durhamensis CSCA 57 T and Actinocrinis puniceicyclus DSM 45168 T  have genome sizes of 7.9, 9.6 and 6.7 Mbp, respectively. A phylogenomic tree shows that they form distinct branches in a well-supported clade, a result supported by associated phenotypic data. Average nucleotide identity and digital DNA:DNA hybridization similarities are below the recommended thresholds for assigning strains to the same species; they also indicate that isolate MGRD01-02 T is most closely related to the A. durhamensis and A. robiniae strains. Corresponding amino acid identity and conserved protein data not only support these relationships but also confirm the taxonomic integrity of the genus Actinocrinis. Based on these results, it is proposed that isolate MGRD01-02 T (= CCMM B1308 T = ICEBB-09 T = NCIMB 15218 T ) be classified in the genus Actinospica as Actinospica acidithermotolerans sp. nov. The draft genome of the isolate and its closest phylogenomic neighbours contain biosynthetic gene clusters with the potential to produce new natural products, notably antibiotics., (© 2022. The Author(s).)

A genome led phylophasic study was designed to determine the taxonomic status of a strain, DSM 45956, recovered from a Saharan desert soil. A wealth of taxonomic data, including average nucleotide identity and DNA:DNA hybridization (DDH) values, showed that the isolate and the type strains of Actinopolyspora lacussalsi and Actinopolyspora righensis belong to the same species. Consequently, it is proposed that A. righensis is a heterotypic synonym of A. lacussalsi. Similarly, DDH values and associated phenotypic data show that A. lacussalsi contains two subspecies, A. lacussalsi subsp. lacussalsi and A. lacussalsi subsp. righensis which includes isolate DSM 45956., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

A novel Gram-negative, facultative anaerobic, rod-shaped, and non-motile bacterium with bio-degradation potential of polycyclic aromatic hydrocarbons (PAHs) and uranium bio-reduction, designated as RCRI7 T , was isolated from Qurugöl Lake water near Tabriz city. Strain RCRI7 T can grow in the absence of NaCl and tolerates up to 3% NaCl (optimum, 0-0.5%), at the temperature range of 4-45 °C (optimum, 30 °C) and a pH range of 6-9 (optimum, pH 7 ± 0.5). Results of phylogenetic analysis based on 16S rRNA gene sequence indicated that strain RCRI7 T is affiliated with the genus Shewanella, most closely related to Shewanella xiamenensis S4 T (99.1%) and Shewanella putrefaciens JCM 20190 T (98.9%). The genomic DNA G+C content of strain RCRI7 T is 41 mol%. The major fatty acids are C 16:1 ω9c, C 18:1 ω9c and iso-C 17:1 ω5c. The OrthoANI and ANIb values between RCRI7 T and Shewanella xiamenensis S4 T were 87.4% and 87.7%, and between RCRI7 T and Shewanella putrefaciens JCM 20190 T were 79.5% and 79.7%, respectively. Strain RCRI7 T displayed dDDH values of 30.2% and 39.8% to Shewanella xiamenensis S4 T and Shewanella putrefaciens JCM 20190 T , respectively. The major polar lipids include phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). The respiratory quinone is Q8. Based on the polyphasic evidence presented in this paper, strain RCRI7 T is considered to represent a novel species, with bioremediation potential, in the genus Shewanella, for which the name Shewanella azerbaijanica sp. nov. is proposed. The type strain is RCRI7 T (= JCM 17276 T ) (= KCTC 62476 T )., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

A new actinobacterium strain, designated BMG 823 T , was isolated from a limestone sample collected in Tunisia. Its taxonomic position was scrutinized using a polyphasic approach. Colonies of strain BMG 823 T were pink orange-coloured, regular and had a moist surface. Cells are Gram-stain-positive, catalase-negative and oxidase-negative. The strain grew at pH 5.5-9, 10-40 °C and in presence of up to 4 % NaCl (w/v). Chemotaxonomically, strain BMG 823 T was characterized by cell-wall type III containing meso -diaminopimelic acid as diamino acid, glucose, ribose and rhamnose as whole-cell sugars, MK-9(H 4 ) as predominant menaquinone, and phosphatidylcholine, diphosphadidylglycerol, phosphatidethanolamine, phosphatidylcholine, phosphatidylinositol, unidentified glycolipid, unidentified aminophospholipids and unidentified glycophospholipid as major polar lipids. The fatty acid profile consisted of iso-C 16 : 0 and iso-C 17 : 1  ω 9. Phylogenetic trees based on 16S rRNA gene and genome sequences placed strain BMG 823 T within the genus Blastococcus and separated it from all type strains of validly published species. Comparison of 16S rRNA gene sequence similarity, digital DNA-DNA hybridization and average nucleotide identity indicated that strain BMG 823 T was most closely related to Blastococcus litoris DSM 106127 T and Blastococcus colisei BMG 822 T with pairwise values well below the species differentiation thresholds. The distinct phenotypic and genotypic features of strain BMG 823 T (=DSM 46838 T =CECT 8881 T ) within the genus Blastococcus warrant its recognition as the type strain for the new species for which we propose the name Blastococcus tunisiensis sp. nov.

A genome-based polyphasic study was undertaken to establish the taxonomic status of an actinobacterium strain isolated from an actinorhizal root nodule. Strain ncl1 T was found to have chemotaxonomic, cultural and morphological properties characteristic of members of the genus Nocardia. The strain was closely related to Nocardia aurea in the phylogenetic trees based on 16S rRNA gene and genome sequences. The draft genome of the strain is 8.9 Mbp in size, has a genomic DNA G + C content of 67.0% and was predicted to contain at least 19 biosynthetic gene clusters encoding for specialized metabolites. Strain ncl1 T was distinguished from its closest neighbour, N. aurea DSM 103986 T , by a broad range of phenotypic properties and by low average nucleotide identity and digital DNA-DNA hybridization scores. Consequently, the strain represents a novel Nocardia species for which the name Nocardia noduli sp. nov. is proposed. The type strain is ncl1 T (CECT 30123 T  = DSM 110878 T ). The present study provides further evidence that actinorhizal nodules are a source of novel species of Nocardia., (© 2022. The Author(s).)

An actinobacterial strain A23 T , isolated from adult ant Camponotus vagus collected in Ryazan region (Russia) and established as tetracenomycin X producer, was subjected to a polyphasic taxonomic study. Morphological characteristics of this strain included well-branched substrate mycelium and aerial hyphae fragmented into rod-shaped elements. Phylogenetic analyses based on 16S rRNA gene and genome sequences showed that strain A23 T was most closely related to Amycolatopsis pretoriensis DSM 44654 T . Average nucleotide identity and digital DNA-DNA hybridization values between the genome sequences of isolate A23 T and its closest relative, Amycolatopsis pretoriensis DSM 44654 T , were 39.5% and 88.6%, which were below the 70% and 95-96% cut-off point recommended for bacterial species demarcation, respectively. The genome size of the isolate A23 T was 10,560,374 bp with a DNA G + C content of 71.2%. The whole-cell hydrolysate contained meso-diaminopimelic acid and arabinose and galactose as main diagnostic sugars as well as ribose and rhamnose. It contained MK-9(H4) as the predominant menaquinone and iso-C 16:0 , iso-C 15:0 , anteiso-C 17:0 and C 16:0 as the major cellular fatty acids. Diphosphatidylglycerol and phosphatidylethanolamine prevailed among phospholipids. Mycolic acids were not detected. Based on the phenotypic, genomic and phylogenetic data, isolate A23 T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis camponoti sp. nov. is proposed, and the type strain is A23 T (= DSM 111725 T  = VKM 2882 T )., (© 2022. The Author(s).)

Background: Recent studies highlighted the biosynthetic potential of nocardiae to produce diverse novel natural products comparable to that of Streptomyces, thereby making them an attractive source of new drug leads. Many of the 119 Nocardia validly named species were isolated from natural habitats but little is known about the diversity and the potential of the endophytic nocardiae of root nodule of actinorhizal plants., Results: The taxonomic status of an actinobacterium strain, designated ncl2 T , was established in a genome-based polyphasic study. The strain was Gram-stain-positive, produced substrate and aerial hyphae that fragmented into coccoid and rod-like elements and showed chemotaxonomic properties that were also typical of the genus Nocardia. It formed a distinct branch in the Nocardia 16S rRNA gene tree and was most closely related to the type strains of Nocardia nova (98.6%), Nocardia jiangxiensis (98.4%), Nocardia miyuensis (97.8%) and Nocardia vaccinii (97.7%). A comparison of the draft genome sequence generated for the isolate with the whole genome sequences of its closest phylogenetic neighbours showed that it was most closely related to the N. jiangxiensis, N. miyuensis and N. vaccinii strains, a result underpinned by average nucleotide identity and digital DNA-DNA hybridization data. Corresponding taxogenomic data, including those from a pan-genome sequence analysis showed that strain ncl2 T was most closely related to N. vaccinii DSM 43285 T . A combination of genomic, genotypic and phenotypic data distinguished these strains from one another. Consequently, it is proposed that strain ncl2 T (= DSM 110931 T = CECT 30122 T ) represents a new species within the genus Nocardia, namely Nocardia alni sp. nov. The genomes of the N. alni and N. vaccinii strains contained 36 and 29 natural product-biosynthetic gene clusters, respectively, many of which were predicted to encode for a broad range of novel specialised products, notably antibiotics. Genome mining of the N. alni strain and the type strains of its closest phylogenetic neighbours revealed the presence of genes associated with direct and indirect mechanisms that promote plant growth. The core genomes of these strains mainly consisted of genes involved in amino acid transport and metabolism, energy production and conversion and transcription., Conclusions: Our genome-based taxonomic study showed that isolate ncl2 T formed a new centre of evolutionary variation within the genus Nocardia. This novel endophytic strain contained natural product biosynthetic gene clusters predicted to synthesize novel specialised products, notably antibiotics and genes associated with the expression of plant growth promoting compounds., (© 2021. The Author(s).)

Advanced physicochemical and chemical absorption methods for chlorinated ethenes are feasible but incur high costs and leave traces of pollutants on the site. Biodegradation of such pollutants by anaerobic or aerobic bacteria is emerging as a potential alternative. Several mycobacteria including Mycolicibacterium aurum L1, Mycolicibacterium chubuense NBB4, Mycolicibacterium rhodesiae JS60, Mycolicibacterium rhodesiae NBB3 and Mycolicibacterium smegmatis JS623 have previously been described as assimilators of vinyl chloride (VC). In this study, we compared nucleotide sequence of VC cluster and performed a taxogenomic evaluation of these mycobacterial species. The results showed that the complete VC cluster was acquired by horizontal gene transfer and not intrinsic to the genus Mycobacterium sensu lato . These results also revealed the presence of an additional xcb F1 gene that seems to be involved in Coenzyme M biosynthesis, which is ultimately used in the VC degradation pathway. Furthermore, we suggest for the first time that S/N-Oxide reductase encoding gene was involved in the dissociation of the SsuABC transporters from the organosulfur, which play a crucial role in the Coenzyme M biosynthesis. Based on genomic data, M. aurum L1, M. chubuense NBB4 , M. rhodesiae JS60, M. rhodesiae NBB3 and M. smegmatis JS623 were misclassified and form a novel species within the genus Mycobacterium sensu lato . Mycolicibacterium aurum L1 T (CECT 8761 T  = DSM 6695 T ) was the subject of polyphasic taxonomic studies and showed ANI and dDDH values of 84.7 and 28.5% with its close phylogenetic neighbour, M. sphagni ATCC 33027 T . Phenotypic, chemotaxonomic and genomic data considering strain L1 T (CECT 8761 T  = DSM 6695 T ) as a type strain of novel species with the proposed name, Mycolicibacterium vinylchloridicum sp. nov., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Cortés-Albayay, Sangal, Klenk and Nouioui.)

Over the last few decades, a wealth of evidence has formed the basis for "the Old Friends hypothesis" suggesting that, in contrast to the past, increasingly people are living in environments with limited and less diverse microbial exposure, with potential consequences for their health. Hence, including safe live or heat-killed microbes in the diet may be beneficial in promoting and maintaining human health. In order to assess the safety of microbes beyond the current use of standardized cultures and probiotic supplements, new approaches are being developed. Here, we present evidence for the safety of heat-killed Mycolicibacterium aurum Aogashima as a novel food, utilizing the decision tree approach developed by Pariza and colleagues (2015). We provide evidence that the genome of M. aurum Aogashima is free of (1) genetic elements associated with pathogenicity or toxigenicity, (2) transferable antibiotic resistance gene DNA, and (3) genes coding for antibiotics used in human or veterinary medicine. Moreover, a 90-day oral toxicity study in rats showed that (4) the no observed adverse effect level (NOAEL) was the highest concentration tested, namely 2000  μ g/kg BW/day. We conclude that oral consumption of heat-killed M . aurum Aogashima is safe and warrants further evaluation as a novel food ingredient., Competing Interests: TD is a senior executive and holds stock in Aurum Switzerland AG. IN has no conflict of interest to declare., (© 2021 Aurum Switzerland AG. Food Science & Nutrition published by Wiley Periodicals LLC.)

Yellow-eyed penguins, Megadyptes antipodes, are an endangered species that are endemic to New Zealand. Outbreaks of diphtheritic stomatitis have caused significant mortality for this species, especially among young chicks. In this study, we isolated 16 Corynebacterium sp. isolates from the oral cavities of 2- to 14-day-old chicks at a range of infection stages and sequenced the genomes to understand their virulence mechanisms. Phylogenomic and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) characterization indicate that these strains belong to a novel Corynebacterium species. A simple multiplex PCR-based diagnostic assay has been developed to identify these strains rapidly and reliably. Similar to other corynebacteria, genomic islands and prophages introduced significant diversity among these strains that has potentially led to minor functional variations between the two lineages. Despite the presence of multiple corynebacterial virulence genes and a spaDEF -type pilus gene cluster among these strains, the survival rate was much higher in Galleria mellonella larvae than in those inoculated with Corynebacterium ulcerans NZRM 818 and Corynebacterium pseudotuberculosis NZRM 3004. Therefore, these strains are opportunistic pathogens causing high mortality among young penguin chicks due to a less-developed immune system. IMPORTANCE Yellow-eyed penguins, Megadyptes antipodes, are endangered species with a sharp decline in the numbers of breeding pairs over the last 2 decades. Diphtheritic stomatitis, characterized by a thick fibrinopurulent exudate in the oral cavities and symptoms, including inanition and significant weight loss, is responsible for significant mortality among the young chicks. These chicks are treated with antibiotics, amoxicillin-clavulanic acid or enrofloxacin, but do not always recover from the infection. The pathogen causing these infections and the mechanism of pathogenesis are unclear. This study has identified a novel Corynebacterium species to be associated with diphtheritic stomatitis in yellow-eyed penguins with potential virulence genes that are likely involved in pathogenesis. Importantly, a gene encoding an exotoxin, phospholipase D, is present among these strains. The inactivated form of this enzyme could potentially be used as an effective vaccine to protect these penguins from infection.

A polyphasic study was designed to determine the taxonomic provenance of a strain, isolate PRKS01-29 T , recovered from an Indonesian sand dune and provisionally assigned to the Streptomyces violaceusniger clade. Genomic, genotypic and phenotypic data confirmed this classification. The isolate formed an extensively branched substrate mycelium which carried aerial hyphae that differentiated into spiral chains of rugose ornamented spores, contained LL-as the wall diaminopimelic acid, MK-9 (H 6 , H 8 ) as predominant isoprenologues, phosphatidylethanolamine as the diagnostic phospholipid and major proportions of saturated, iso- and anteiso- fatty acids. Whole-genome sequences generated for the isolate and Streptomyces albiflaviniger DSM 41598 T and Streptomyces javensis DSM 41764 T were compared with phylogenetically closely related strains, the isolate formed a branch within the S. violaceusniger clade in the resultant phylogenomic tree. Whole-genome sequences data showed that isolate PRKS01-29 T was most closely related to the S. albiflaviniger strain but was distinguished from the latter and from other members of the clade using combinations of phenotypic properties and average nucleotide identity and digital DNA:DNA hybridization scores. Consequently, it is proposed that isolate PRKS01-29 T (= CCMM B1303 T  = ICEBB-02 T  = NCIMB 15210 T ) should be classified in the genus Streptomyces as Streptomyces sabulosicollis sp. nov. It is also clear that streptomycetes which produce spiral chains of rugose ornamented spores form a well-defined monophyletic clade in the Streptomyces phylogenomic tree., the taxonomic status of which requires further study. The genome of the type strain of S. sabulosicollis contains biosynthetic gene clusters predicted to produce new natural products.

A Micromonospora strain, isolate MT25 T , was recovered from a sediment collected from the Challenger Deep of the Mariana Trench using a selective isolation procedure. The isolate produced two major metabolites, n -acetylglutaminyl glutamine amide and desferrioxamine B, the chemical structures of which were determined using 1D and 2D-NMR, including 1 H- 15 N HSQC and 1 H- 15 N HMBC 2D-NMR, as well as high resolution MS. A whole genome sequence of the strain showed the presence of ten natural product-biosynthetic gene clusters, including one responsible for the biosynthesis of desferrioxamine B. Whilst 16S rRNA gene sequence analyses showed that the isolate was most closely related to the type strain of Micromonospora chalcea , a whole genome sequence analysis revealed it to be most closely related to Micromonospora tulbaghiae 45142 T . The two strains were distinguished using a combination of genomic and phenotypic features. Based on these data, it is proposed that strain MT25 T (NCIMB 15245 T , TISTR 2834 T ) be classified as Micromonospora provocatoris sp. nov. Analysis of the genome sequence of strain MT25 T (genome size 6.1 Mbp) revealed genes predicted to responsible for its adaptation to extreme environmental conditions that prevail in deep-sea sediments.

Isolate 4NS15 T was isolated from a neglected arid habitat in Kerman, Iran. The strain showed 16S rRNA gene sequence similarity values of 98.9 % to the type strains of Kibdelosporangium aridum subsp. aridum , Kibdelosporangium phytohabitans and Kibdelosporangium philippinense and 98.6 % to the type strain K. aridum subsp. largum , respectively. Genome-based phylogenetic analysis revealed that isolate 4NS15 T is closely related to Kibdelosporangium aridum subsp. aridum DSM 43828 T . The digital DNA-DNA hybridization value between the genome sequences of 4NS15 T and strain DSM 43828 T is 29.8 %. Strain 4NS15 T produces long chains of spores without a sporangium-like structure which can be distinguished from other Kibdelosporangium species. Isolate 4NS15 T has a genome size of 10.35 Mbp with a G+C content of 68.1 mol%. Whole-cell hydrolysates of isolate 4NS15 T are rich in meso -diaminopimelic acid and cell-wall sugars such as arabinose, galactose, glucose and ribose. Major fatty acids (>10 %) are C 16 : 0 , iso-C 16 : 0 and iso-C 15 : 0 . The phospholipid profile contains diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylhydroxyethanolamine, aminolipid and glycoaminolipid. The predominant menaquinone is MK-9(H 4 ). Based on its phenotypic and genotypic characteristics, isolate 4NS15 T (NCCB 100701=CIP 111705=DSM 110728) merits recognition as representing a novel species of the genus Kibdelosporangium , for which the name Kibdelosporangium persicum sp. nov. is proposed.

A new strain belonging to the genus Kocuria, designed PT10, was isolated from irradiated roots of the xerophyte Panicum turgidum. Isolate PT10 is a Gram-positive, coccoid, aerobic and ionizing-radiation (IR)-resistant actinobacterium. PT10 has shown an ability to survive under extreme conditions, such as gamma irradiation, desiccation and high concentration of hydrogen peroxide. Phenotypic, chemotaxonomic and comparative genome analyses support the assignment of strain PT10 (LMG 31102 = DSM 108617) as Kocuria rhizophila. The complete genome sequence of PT10 consists of one chromosome (2,656,287 bps), with a 70.7% G + C content and comprises 2481 protein-coding sequences. A total of 1487 proteins were identified by LC-MS/MS profiling. In silico analyses revealed that the proteome of the oxidation-tolerant PT10 possesses several features explaining its IR-resistant phenotype and many adaptive pathways implicated in response to environmental pressures - desiccation, cold, reactive oxygen species and other stressors., (Copyright © 2020 Elsevier Inc. All rights reserved.)

A novel strain of the genus Promicromonospora, designated PT9 T , was recovered from irradiated roots of the xerophyte Panicum turgidum collected from the Ksar Ghilane oasis in southern Tunisia. Strain PT9 T is aerobic, non-spore-forming, Gram- positive actinomycete that produces branched hyphae and forms white to yellowish-white colonies. Chemotaxonomic features, including fatty acids, whole cell sugars and polar lipid profiles, support the assignment of PT9 T to the genus Promicromonospora. The genomic relatedness indexes based on DNA-DNA hybridization and average nucleotide identity values revealed a significant genomic divergence between strain PT9 T and all sequenced type strains of the taxon. Phylogenomic analysis showed that isolate PT9 T was most closely related to Promicromonospora soli CGMCC 4.7398 T . Phenotypic and phylogenomic analyses suggest that isolate PT9 T represents a novel species of the genus Promicromonospora, for which the name Promicromonospora panici sp. nov. is proposed. The type strain is PT9 T (LMG 31103 T  = DSM 108613 T ).The isolate PT9 T is an ionizing-radiation-resistant actinobacterium (D 10 value = 2.6 kGy), with resistance to desiccation and hydrogen peroxide. The complete genome sequence of PT9 T consists of 6,582,650 bps with 71.2% G+C content and 6291 protein-coding sequences. This genome will help to decipher the microbial genetic bases for ionizing-radiation resistance mechanisms including the response to oxidative stress.

A polyphasic study was undertaken to establish the taxonomic position of six representative streptomycetes isolated from an alkaline soil adjacent to a meteoric alkaline soda lake in India. Chemotaxonomic, cultural and morphological properties of the isolates were consistent with their classification in the genus Streptomyces. The isolates formed extensively branched substrate mycelia and aerial hyphae that differentiated in straight chains of spores with smooth surfaces. They contained LL-diaminopimelic acid in the wall peptidoglycan, produced either hexa- or octa-hydrogenated menaquinones with nine isoprene units, major amounts of saturated, iso- and anteiso- fatty acids and phosphatidylethanolamine as the characteristic polar lipid. The isolates grew well at 30 °C, pH 9 and in the presence of 3 to 5% (w/v) sodium chloride. Isolates OF1 T , OF3 and OF8 formed a distinct clade within the Streptomyces 16S rRNA gene tree sharing relatively high sequence similarities with the type strains of Streptomyces durbertensis (99.3%), Streptomyces palmae (98.1%) and Streptomyces xinghaiensis (98.3%), but can be distinguished from them using combinations of phenotypic properties. A phylogenomic tree based on draft genome sequences of the isolates and S. durbertensis DSM 104538 T confirmed the phylogenetic relationships. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values calculated from the whole genome sequences of isolate OF1 T and S. durbertensis DSM 104538 T were low at 92.0% and 45.2%, respectively, indicating that they belong to different genomic species. Consequently, on the basis of the genomic, phylogenetic and associated phenotypic data it is proposed that isolates OF1 T , OF3 and OF8 be assigned to the genus Streptomyces as Streptomyces alkaliterrae sp. nov. with strain OF1 T (NCIMB 15195 T =PCM 3001 T ) as the type strain. Isolates IF11, IF17 and IF19, and S. alkaliphilus DSM 42118 T were shown to belong to the same taxospecies and together with S. calidiresistens DSM 42108 T comprised a well supported clade in the Streptomyces 16S rRNA gene tree. Isolate IF17 and S. alkaliphilus DSM 42118 T formed a well-supported clade in the phylogenomic tree, had almost identical digital G + C similarity values, produced long straight chains of smooth-surfaced spores and shared ANI and dDDH values (98.0 and 79.6%, respectively) consistent with their assignment to the same genomic species. In light of all of the data isolates IF11, IF17 and IF19 should be seen as authentic stains of S. alkalihilus. Data acquired in the present study have also been used to emend the descriptions of S. alkaliphilus, S. calidiresistens and S. durbertensis. The genomes of isolates IF17, and OF1 T , OF3 and OF8 contain relatively high numbers of biosynthetic gene clusters some of which were discontinously distributed indicating ones predicted to express for novel specialised metabolites., (Copyright © 2020 Elsevier GmbH. All rights reserved.)

Strains 335427 T and 234509 T , isolated from two 76-year-old patients with chronic pulmonary diseases, were the subject of polyphasic taxonomic studies and comparative genomic analyses for virulence factors. The 16 rRNA gene sequence similarity between strains 335427 T and 234509 T and their closest phylogenetic neighbors Nocardia asiatica NBRC 100129 T and Nocardia abscessus NBRC 100374 T were 99.5% and 100%, respectively. Digital DNA-DNA hybridization values between the aforementioned studied strains were well below the 70% threshold for assigning prokaryotic strains to a novel species. Strains 335427 T and 234509 T have genome sizes of 8.49 Mpb and 8.07 Mpb, respectively, with G + C content of 68.5%. Isolate 335427 T has C 16:0 , C 18:1 ω 9 c, C 18:0 and C 18:0 10 methyl as major fatty acids (>15%) and mycolic acids formed of 52-54 carbon atoms. However, only C 18:1 ω 9 c was detected for isolate 234509 T , which had mycolic acids with 44-56 carbon. Based on phenotypic and genetic data, strains 335427 T (DSM 109819 T = CECT 9924 T ) and 234509 T (DSM 111366 T = CECT 30129 T ) merit recognition as novel species, which are named Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., respectively. All the strains studied had homologous VF-associated genes to those described in M. tuberculosis , including experimentally verified virulence genes in humans related to tuberculosis. The nar GHIJ (nitrate reduction pathway) and gvp AFGOJLMK (gas vesicles) genetic maps of strains 335427 T , 234509 T , NBRC 100129 T and NBRC 100374 T showed the same syntenic block and raise the question of whether their functions are interlinked during the infection of the human host. However, further research is required to decipher the role of the gas vesicle in the pathogenicity mechanism of Nocardia spp.

A polyphasic study was undertaken to establish the position of a Streptomyces strain, isolate PRKS01-65 T , recovered from sand dune soil collected at Parangkusumo, Yogyakarta Province, Java, Indonesia. A combination of chemotaxonomic, cultural and morphological properties confirmed its position in the genus of Streptomyces . Comparative 16S rRNA gene sequence analyses showed that the isolate was most closely related to Streptomyces leeuwenhoekii C34 T (99.9 % similarity) and loosely associated with the type strains of Streptomyces chiangmaiensis (98.7 % similarity) and Streptomyces glomeratus (98.9 % similarity). Multilocus sequence analyses based on five conserved housekeeping gene alleles confirmed the close relationship between the isolate and S. leeuwenhoekii C34 T , although both strains belonged to a well-supported clade that encompassed the type strains of S. glomeratus , Streptomyces griseomycini , Streptomyces griseostramineus , Streptomyces labedae , Streptomyces lomondensis and Streptomyces spinoverrucosus . A comparison of the draft genome sequence generated for the isolate with corresponding whole genome sequences of its closest phylogenomic neighbours showed that it formed a well-separated lineage with S. leeuwenhoekii C34 T . These strains can also be distinguished using a combination of phenotypic properties and by average nucleotide identity and digital DNA-DNA hybridization similarities of 94.3 and 56 %, values consistent with their classification in different species. Based on this wealth of data it is proposed that isolate PRKS01-65 T (=NCIMB 15211 T =CCMM B1302 T =ICEBB-03 T ) be classified as Streptomyces harenosi sp. nov. The genome of the isolate contains several biosynthetic gene clusters with the potential to produce new natural products.

A novel actinobacterial strain, designated NA12 T , was isolated from coastal sediment sample of Nemrut Lake, a crater lake in eastern Anatolia, Turkey. The taxonomic position of the strain was established using a polyphasic approach. Cultural and chemotaxonomic characteristics of the strain were consistent with its classification within the family Micromonosporaceae. The 16S rRNA gene sequence analysis of strain NA12 T showed that the strain closely related to M. radicis AZ1-13 T , M. zingiberis PLAI 1-1 T , M. craniella LHW63014 T and M. endophytica 202201 T with pairwise sequence identity values ranging from 99.4 to 99.3%. Digital DNA-DNA hybridization values between strain NA12 T and the closely related type strains were ranged from 41.0 to 18.3% while the average nucleotide identity values were between 87.3 and 86.5%, which are well below the designed cut-off points of 70 and 95%, respectively. The G + C content of genomic DNA was 71.5%. Whole-cell hydrolysates of strain NA12 T contained 3-hydroxydiaminopimelic acid and meso-diaminopimelic acid. Cell-wall sugars were composed of arabinose, fucose, glucose, mannose, rhamnose and xylose. The polar lipid profile contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, glycophospholipid, amino-phospholipid and two unidentified phospholipids. The predominant menaquinones were MK-9(H 6 ) and MK-9(H 4 ). Major fatty acids were iso-C 16:0 and C 17:1 ω8c. Based upon the consensus of phenotypic and phylogenetic analyses as well as whole genome comparisons, strain NA12 T (DSM 100982 T  = KCTC 39647 T ) is proposed to represent the type strain of a novel species, Micromonospora craterilacus sp. nov.

A novel Gram-negative, aerobic, motile and rod-shaped bacterium with the potential to biodegrade polycyclic aromatic hydrocarbons, was isolated from Khazar (Caspian) Sea. Strain TBZ2 T grows in the absence of NaCl and tolerates up to 8.5% NaCl. Growth occurred at pH 3.0-10.0 (optimum, pH 6.0-7.0) and 10-45 °C (optimum, 30 °C). The major fatty acids are C 18:1 ω7C, C 16:1 ω7C/ C 15:0 iso 2-OH, C 16:0 , C 12:0, C 10:0 3-OH, C 12:0 3-OH. The major polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and the predominant respiratory quinone is ubiquinone Q-9. The 16S rRNA gene sequence analysis showed that strain TBZ2 T is a member of the genus Pseudomonas with the highest similarity to P. oleovorans subsp. oleovorans DSM 1045 T (98.83%), P. mendocina NBRC 14162 T (98.63%), P. oleovorans subsp. lubricantis RS1 T (98.61%) and P. alcaliphila JCM 10630 T (98.49%) based on EzBioCloud server. Phylogenetic analyses using housekeeping genes (16S rRNA, rpoD, gyrB and rpoB) and genome sequences demonstrated that the strain TBZ2 T formed a distinct branch closely related to the type strains of P. mendocina and P. guguanensis. Digital DNA-DNA hybridisation and average nucleotide identity values between strain TBZ2 T and its closest relatives, P. mendocina NBRC 14162 T (25.3%, 81.5%) and P. guguanensis JCM 18146 T (26.8%, 79.0%), rate well below the designed threshold for assigning prokaryotic strains to the same species. On the basis of phenotypic, chemotaxonomic, genomic and phylogenetic results, it is recommended that strain TBZ2 T is a novel species of the genus Pseudomonas, for which the name Pseudomonas khazarica sp. nov., is proposed. The type strain is TBZ2 T (= LMG 29674 T  = KCTC 52410 T ).

Dermacoccus abyssi strain MT1.1 T is a piezotolerant actinobacterium that was isolated from Mariana Trench sediment collected at a depth of 10898 m. The organism was found to produce ten dermacozines (A‒J) that belonged to a new phenazine family and which displayed various biological activities such as radical scavenging and cytotoxicity. Here, we report on the isolation and identification of a new dermacozine compound, dermacozine M, the chemical structure of which was determined using 1D and 2D-NMR, and high resolution MS. A whole genome sequence of the strain contained six secondary metabolite-biosynthetic gene clusters (BGCs), including one responsible for the biosynthesis of a family of phenazine compounds. A pathway leading to the biosynthesis of dermacozines is proposed. Bioinformatic analyses of key stress-related genes provide an insight into how the organism adapted to the environmental conditions that prevail in the deep-sea.

Actinobacterial strain Cj T was directly isolated from soil beneath Ceanothus jepsonii growing in the USA. The strain formed cell structures typical of the genus Frankia including extensive hyphae, vesicles and sporangia, and it effectively nodulated members of the actinorhizal Colletieae, Elaeagnaceae and Myricaceae. The whole-cell hydrolysate of strain Cj T was rich in meso -diaminopimelic acid and galactose, glucose, mannose, xylose, ribose and a trace of rhamnose. Tbe polar lipid profile contained phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol and glycophospholipid. The menaquinone was predominantly MK-9(H 4 ). The fatty acid profile predominantly consisted of C 17 : 1 ω8c, iso-C 16 : 0 , C 15:0 , C 16 : 0 and C 17 : 0 . A multilocus sequence analysis phylogeny based on atp 1, fts Z, dna K, gyr A and sec A gene sequences positioned the strain within Elaeagnaceae - and Colletieae-nodulating species together with Frankia elaeagni DSM 46783 T , Frankia discariae DSM 46785 T and Frankia irregularis DSM 45899 T . Pairwise 16S rRNA gene sequence similarities showed that strain Cj T was most closely related to F. discariae DSM 46785 T (99.78 %) while their digital DNA-DNA hybridization value was 41.1 %. Based on the overall analyses, strain Cj T (=DSM 100623 T =CECT 9041 T ) warrants classification as the type strain of a novel species, for which the name Frankia soli sp. nov. is proposed.

Five actinobacteria isolates, KC201 T , KC401, KC310 T , KC712 T and 6K102 T , were recovered from the Karakum Desert during an investigation of novel actinobacteria with biotechnological potential. A polyphasic approach confirmed the affiliation of the strains to the genus Nonomuraea . The strains showed chemotaxonomic and morphological properties consistent with their classification in the genus Nonomuraea . Furthermore, these strains clearly distinguished and formed well supperted clades in phylogenetic and phylogenomic trees. Low ANI and dDDH values and distinguishing phenotypic properties between isolates KC201 T , KC310 T , KC712 T and 6K102 T showed that these strains belonged to novel Nonomuraea species, the names proposed for these taxa are Nonomuraea deserti sp. nov., Nonomuraea diastatica sp. nov., Nonomuraea longispora sp. nov. and Nonomuraea mesophila sp. nov., with the type strains KC310 T (=CGMCC 4.7331 T =DSM 102919 T =KCTC 39774 T ), KC712 T (=CGMCC 4.7334 T =DSM 102925 T =KCTC 39776), KC201 T (=CGMCC 4.7339 T =DSM 102917 T =KCTC 39781 T ) and 6K102 T (=CGMCC 4.7541 T =JCM 32916), respectively.

A set of oligonucleotide primers, Rubro223f and Rubro454r, were found to amplify a 267 nucleotide sequence of 16S rRNA genes of Rubrobacter type strains. The primers distinguished members of this genus from other deeply-rooted actinobacterial lineages corresponding to the genera Conexibacter, Gaiella, Parviterribacter, Patulibacter, Solirubrobacter and Thermoleophilum of the class Thermoleophilia. Amplification of DNA bands of about 267 nucleotides were generated from environmental DNA extracted from soil samples taken from two locations in the Atacama Desert. Sequencing of a DNA library prepared from the bands showed that all of the clones fell within the evolutionary radiation occupied by the genus Rubrobacter. Most of the clones were assigned to two lineages that were well separated from phyletic lines composed of Rubrobacter type strains. It can be concluded that primers Rubro223f and Rubro454r are specific for the genus Rubrobacter and can be used to detect the presence and abundance of members of this genus in the Atacama Desert and other biomes.

A Micromonospora strain, designated 5R2A7 T , isolated from a high altitude Atacama Desert soil was examined by using a polyphasic approach. Strain 5R2A7 T was found to have morphological, chemotaxonomic and cultural characteristics typical of members of the genus Micromonospora. The cell wall contains meso - and hydroxy -diaminopimelic acid, the major whole-cell sugars are glucose, ribose and xylose, the predominant menaquinones MK-10(H 4 ), MK-10(H 6 ), MK-10(H 8 ) and MK-9(H 6 ), the major polar lipids diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and an unknown glycolipid, and the predominant cellular fatty acids iso -C 16 : 0 , iso -C 15 : 0 and 10-methyl C 17 : 0 . The digital genomic DNA G+C content is 72.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain 5R2A7 T was closely related to Micromonospora coriariae DSM 44875 T (99.8 %) and Micromonospora cremea CR30 T (99.7 %), and was separated readily from the latter, its closest phylogenetic neighbour, based on gyrB and multilocus sequence data, by low average nucleotide identity (92.59 %) and in silico DNA-DNA relatedness (51.7 %) values calculated from draft genome assemblies and by a range of chemotaxonomic and phenotypic properties. Consequently, strain 5R2A7 T is considered to represent a novel species of Micromonospora for which the name Micromonospora acroterricola sp. nov. is proposed. The type strain is 5R2A7 T (=LMG 30755 T =CECT 9656 T ).