Rhodococcus soli sp. nov., an actinobacterium isolated from soil using a resuscitative technique

Complete genome sequence of the saprophytic actinomycete Rhodococcus (Prescottella) soli DSD51WT, closely related to the multi-host pathogen Rhodococcus (Prescottella) equi

Rhodococcus (Prescottella) soli strain DSD51WT is an aerobic, non-spore-forming, non-motile actinomycete isolated previously from soil collected from Kyoto Park, Japan, using a resuscitative technique. Here, we report the complete, circular genome sequence of R. soli DSD51WT. We employed a hybrid approach using Illumina and Oxford Nanopore platforms.

Is the bacterial genus name Rhodococcus Zopf 1891 illegitimate? Request for an Opinion

In 2014, it was reported that the bacterial genus name Rhodococcus Zopf 1891 was illegitimate due to the priority of the cyanobacterial genus name Rhodococcus Hansgirg 1884. Since that time, the consequences of this conclusion have been largely ignored, whilst changes have been made to relevant Rules of the International Code of Nomenclature of Prokaryotes, including significant changes to the way in which the Code treats the names of members of Cyanobacteriota. Given the complexity of the nomenclatural issues, we request the opinion of the Judicial Commission of the International Committee on Systematics of Prokaryotes as to whether the genus name Rhodococcus Zopf 1891 (Approved Lists 1980) is illegitimate.

The resuscitation-promoting factor (Rpf) from Micrococcus luteus and its putative reaction product 1,6-anhydro-MurNAc increase culturability of environmental bacteria

Dormant bacterial cells do not divide and are not immediately culturable, but they persist in a state of low metabolic activity, a physiological state having clinical relevance, for instance in latent tuberculosis. Resuscitation-promoting factors (Rpfs) are proteins that act as signalling molecules mediating growth and replication. In this study we aimed to test the effect of Rpfs from Micrococcus luteus on the number and diversity of cultured bacteria using insect and soil samples, and to examine if the increase in culturability could be reproduced with the putative reaction product of Rpf, 1,6-anhydro-N-acetylmuramic acid (1,6-anhydro-MurNAc). The rpf gene from Micrococcus luteus was amplified and cloned into a pET21b expression vector and the protein was expressed in Escherichia coli BL21(DE3) cells and purified by affinity chromatography using a hexa-histidine tag. 1,6-Anhydro-MurNAc was prepared using reported chemical synthesis methods. Recombinant Rpf protein or 1,6-anhydro-MurNAc were added to R2A cultivation media, and their effect on the culturability of bacteria from eight environmental samples including four cockroach guts and four soils was examined. Colony-forming units, 16S rRNA gene copies and Illumina amplicon sequencing of the 16S rRNA gene were measured for all eight samples subjected to three different treatments: Rpf, 1,6-anhydro-MurNAc or blank control. Both Rpf and 1,6-anhydro-MurNAc increased the number of colony-forming units and of 16S rRNA gene copies across the samples although the protein was more effective. The Rpf and 1,6-anhydro-MurNAc promoted the cultivation of a diverse set of bacteria and in particular certain clades of the phyla Actinomycetota and Bacillota . This study opens the path for improved cultivation strategies aiming to isolate and study yet undescribed living bacterial organisms.

A stable home for an equine pathogen: valid publication of the binomial Prescottella equi gen. nov., comb. nov., and reclassification of four rhodococcal species into the genus Prescottella

Opinion 106 of the Judicial Commission has clarified the nomenclature of the taxon variously named Rhodococcus equi , ‘Prescottella equi’ and Rhodococcus hoagii . As a consequence, we present here the genus name Prescottella and that of its nomenclatural type species, Prescottella equi comb. nov., for valid publication and propose the reclassification of four rhodococcal species as novel combinations in the genus, namely Prescottella agglutinans Guo et al. 2015 comb. nov., Prescottella defluvii Kämpfer et al. 2014 comb. nov., Prescottella soli Li et al. 2015 comb. nov. and Prescottella subtropica Lee et al. 2019 comb. nov. In addition, we note that a clinical isolate, strain 86–07 (=W8901), likely represents an additional species within the genus Prescottella . Nearly a century after the original description of the type strain of the type species as Corynebacterium equi , we provide a stable home for Prescottella equi and its relatives.

Genomic Characteristics Revealed Plasmid-Mediated Pathogenicity and Ubiquitous Rifamycin Resistance of Rhodococcus equi

Rhodococcus equi is a zoonotic pathogen that can cause fatal disease in patients who are immunocompromised. At present, the epidemiology and pathogenic mechanisms of R. equi infection are not clear. This study characterized the genomes of 53 R. equi strains from different sources. Pan-genome analysis showed that all R. equi strains contained 11481 pan genes, including 3690 core genes and 602 ~ 1079 accessory genes. Functional annotation of pan genome focused on the genes related to basic lifestyle, such as the storage and expression of metabolic and genetic information. Phylogenetic analysis based on pan-genome showed that the R. equi strains were clustered into six clades, which was not directly related to the isolation location and host source. Also, a total of 84 virulence genes were predicted in 53 R. equi strains. These virulence factors can be divided into 20 categories related to substance metabolism, secreted protein and immune escape. Meanwhile, six antibiotic resistance genes (RbpA, tetA (33), erm (46), sul1, qacEdelta 1 and aadA9) were detected, and all strains carried RbpA related to rifamycin resistance. In addition, 28 plasmids were found in the 53 R. equi strains, belonging to Type-A (n = 14), Type-B (n = 8) and Type-N (n = 6), respectively. The genetic structures of the same type of plasmid were highly similar. In conclusion, R. equi strains show different genomic characteristics, virulence-related genes, potential drug resistance and virulence plasmid structures, which may be conducive to the evolution of its pathogenesis.

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

Global environmental contamination with a complex mixture of xenobiotics has become a major environmental issue worldwide. Many xenobiotic compounds severely impact the environment due to their high toxicity, prolonged persistence, and limited biodegradability. Microbial-assisted degradation of xenobiotic compounds is considered to be the most effective and beneficial approach. Microorganisms have remarkable catabolic potential, with genes, enzymes, and degradation pathways implicated in the process of biodegradation. A number of microbes, including Alcaligenes, Cellulosimicrobium, Microbacterium, Micrococcus, Methanospirillum, Aeromonas, Sphingobium, Flavobacterium, Rhodococcus, Aspergillus, Penecillium, Trichoderma, Streptomyces, Rhodotorula, Candida, and Aureobasidium, have been isolated and characterized, and have shown exceptional biodegradation potential for a variety of xenobiotic contaminants from soil/water environments. Microorganisms potentially utilize xenobiotic contaminants as carbon or nitrogen sources to sustain their growth and metabolic activities. Diverse microbial populations survive in harsh contaminated environments, exhibiting a significant biodegradation potential to degrade and transform pollutants. However, the study of such microbial populations requires a more advanced and multifaceted approach. Currently, multiple advanced approaches, including metagenomics, proteomics, transcriptomics, and metabolomics, are successfully employed for the characterization of pollutant-degrading microorganisms, their metabolic machinery, novel proteins, and catabolic genes involved in the degradation process. These technologies are highly sophisticated, and efficient for obtaining information about the genetic diversity and community structures of microorganisms. Advanced molecular technologies used for the characterization of complex microbial communities give an in-depth understanding of their structural and functional aspects, and help to resolve issues related to the biodegradation potential of microorganisms. This review article discusses the biodegradation potential of microorganisms and provides insights into recent advances and omics approaches employed for the specific characterization of xenobiotic-degrading microorganisms from contaminated environments.

Marmoricola caldifontis sp. nov., a novel actinobacterium isolated from a hot spring

A Gram-staining-positive, aerobic, non-motile, non-spore-forming and coccoid-shaped actinobacterial strain, designated YIM 730233^T, was isolated from a sediment sample, collected from a hot spring in Tibet, China. Colonies were brownish, circular, smooth and convex. Strain YIM 730233^T was able to grow in the temperature range of 20-50 °C, pH 6.5-8.0 and in the presence of up to 1.0 % (w/v) NaCl. A comparison of the 16S rRNA gene sequence of strain YIM 730233^T with sequences of type strains of most closely related species of Marmoricola showed highest sequence similarities to Marmoricola bigeumensis MSL-05^T (98.3%) and Marmoricola pocheonensis Gsoil 818^T (98.1%). The draft genome of strain YIM 730233^T had a size of 4 806 234 bp with a DNA G+C content of 72.1 mol%. The major fatty acids (>10 %) of strain YIM 730233^T mainly consisted of iso-C_16 : 0, anteiso-C_17 : 0 and C_18 : 1 ω9c, typical of the genus Marmoricola. Strain YIM 730233^T had LL-2,6-diaminopimelic acid as the diagnostic diamino acid in the cell wall. The predominant isoprenoid quinone was MK-8(H₄). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids and an unidentified lipid. DNA-DNA hybridizations between strain YIM 730233^T and type strains of Marmoricola bigeumensis MSL-05^T and Marmoricola pocheonensis Gsoil 818^T resulted in similarity values of 21 and 19% respectively. Based on DNA-DNA hybridization results, together with the differentiating biochemical and chemotaxonomic features, showed that strain YIM 730233^T represents a novel Marmoricola species, for which the name Marmoricola caldifontis sp. nov. (type strain YIM 730233^T=KCTC 49192^T=CGMCC 4.7521^T), is proposed.

Streptomyces cavernae sp. nov., a novel actinobacterium isolated from a karst cave sediment sample

A novel actinobacterial strain, designated SYSU K10008^T, was isolated from a soil sample collected from a karst cave in Xingyi County, Guizhou Province, south-western PR China. The taxonomic position of the strain was investigated by using a polyphasic approach. Cells of the strain were aerobic, Gram-stain-positive and non-motile. On the basis of 16S rRNA gene sequence similarities and the results of phylogenetic analysis, strain SYSU K10008^T was most closely related to Streptomyces cyaneus CGMCC 4.1671^T, and shared the highest sequence identity of 98.3 % based on the NCBI database. In addition, ll-diaminopimelic acid was the diagnostic diamino acid in cell-wall peptidoglycan. The whole-cell sugars were glucose and rhamnose. The major isoprenoid quinone was MK-9(H₆), while the major fatty acids (>10 %) were C_16 : 0, iso-C_16 : 0, anteiso-C_15 : 0 and summed feature 3 (C_16 : 1 ω7c/C_{16  : 1} ω6c). The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified lipid. The genomic DNA G+C content of strain SYSU K10008^T was 70.5 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K10008^T represents a novel species of the genus Streptomyces, for which the name Streptomyces cavernae sp. nov. is proposed. The type strain is SYSU K10008^T (=KCTC 39850^T=DSM 104115^T).

Rhodococcus subtropicus sp. nov., a new actinobacterium isolated from a cave

A novel Gram-stain-positive actinobacterial strain, designated C9-28^T, was isolated from soil sampled in a natural cave on Jeju Island, Republic of Korea. Strain C9-28^T morphologically exhibited a rod-coccus life cycle and grew at 10-37 °C (optimum, 30 °C), pH 6-9 (optimum, pH 7) and 0-3 % (optimum, absence of NaCl). In the maximum-likelihood tree based on 16S rRNA gene sequences, strain C9-28^T formed a sublineage between a Rhodococcus equi-Rhodococcus soli-Rhodococcus agglutinans clade and the type strain of Rhodococcus defluvii. The closest relatives of strain C9-28^T were the type strains of R. defluvii (98.88 % 16S rRNA gene sequence similarity), R. equi (98.88 %) and R. soli (98.60 %). The phylogenomic tree based on whole genome sequences supported the distinct position of the novel strain within the genus Rhodococcus. The following chemotaxonomic characteristics also supported the assignment to the genus: meso-diaminopimelic acid; arabinose and galactose in whole-cell hydrolysates; the predominant menaquinone of MK-8(H₂); and polar lipids including diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, three unidentified glycolipids and two unidentified lipids. The predominant cellular fatty acids were C_16 : 0, summed feature 3 (C_16 : 1ω7c and/or C_16 : 1ω6c), C_18 : 1ω9c and C_14 : 0. Based on the values of average nucleotide identity and digital DNA-DNA hybridization from whole genome sequences, and in vitro DNA-DNA hybridization between the isolate and the closest relatives, strain C9-28^T (=KACC 19823^T=DSM 107559^T) represents a novel species of the genus Rhodococcus, for which the name Rhodococcussubtropicus sp. nov. is proposed.

Microlunatus speluncae sp. nov., a novel actinobacterium isolated from a Karstic subterranean environment sample

A novel actinobacterial strain, designated SYSU K12189^T, was isolated from a soil sample collected from a Karst cave in Xingyi county, Guizhou province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were observed to be aerobic and Gram-stain positive. On the basis of 16S rRNA gene sequence similarities and phylogenetic analysis, strain SYSU K12189^T is closely related to the type strains of the genus Microlunatus, Microlunatus parietis 12-Be-011^T (98.5% sequence similarity), Microlunatus nigridraconis CPCC 203993^T (98.4%) and Microlunatus cavernae YIM C01117^T (96.6%), and is therefore considered to represent a member of the genus Microlunatus. DNA-DNA hybridization values between strain SYSU K12189^T and related type strains of the genus Microlunatus were < 70%. In addition, LL-diaminopimelic acid was found to be the diagnostic diamino acid in the cell wall peptidoglycan. The major isoprenoid quinone was identified as MK-9(H₄), while the major fatty acids (> 10%) were found to be anteiso-C_15:0, iso-C_15:0, iso-C_16:0 and iso-C_14:0. The polar lipids were found to contain diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, three glycolipids and two unidentified lipids. The genomic DNA G+C content of strain SYSU K12189^T was determined to be 69.4 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K12189^T is concluded to represent a novel species of the genus Microlunatus, for which the name Microlunatus speluncae sp. nov. is proposed. The type strain is SYSU K12189^T (= KCTC 39847^T = DSM 103947^T).

Marinitenerispora sediminis gen. nov., sp. nov., a member of the family Nocardiopsaceae isolated from marine sediment

Three novel actinobacterial strains, designated as TPS16^T, TPS81 and TPS83, were isolated from a sample of marine sediment collected from Tioman Island, Malaysia. The strains formed abundant branched substrate mycelia without fragmentation along with production of blue spores and blue diffusible pigment on soybean meal agar. The strains could grow at pH ranging from pH 6 to 12 and in 0-8 % (w/v) NaCl. Cell-wall hydrolysis showed the presence of meso-diaminopimelic acid. The strains were closely related to Marinactinospora thermotolerans SCSIO 00652^T (97.60 %) and Marinactinospora endophytica YIM 690053^T (96.87 %) based on phylogenetic analysis of 16S rRNA gene sequences. Multilocus sequence analysis including gyrB, recA and rpoB genes further confirmed that strain TPS16^T represented a distinct branch within the family Nocardiopsaceae. The predominant menaquinones were MK-11(H₂), MK-10(H₂), MK-11(H₄) and MK-10(H₄), while the major fatty acids were found to be iso-C_16 : 0, anteiso-C_17 : 0, iso-C_15 : 0 and C_18 : 1ω9c. Genome sequencing revealed genome sizes of approximately 6 Mb and G+C contents of 73.8 mol%. A new genus, Marinitenerispora gen. nov., is proposed within the family Nocardiopsaceae based on polyphasic data and the type species is Marinitenerispora sediminis gen. nov., sp. nov. The type strain is TPS16^T (=DSM 46825^T=TBRC 5138^T).

Aquabacterium tepidiphilum sp. nov., a moderately thermophilic bacterium isolated from a hot spring

A Gram-stain-negative, aerobic, non-spore-forming and rod-shaped bacterium, designated YIM 730274^T, was isolated from a sediment sample collected from a hot spring located in Tibet, PR China, and was characterized by using a polyphasic taxonomy approach. Cells were motile by means of a polar flagellum. The strain was oxidase- and catalase-positive, and contained polyalkanoates and polyphosphate as storage polymers. Growth occurred at 25-50 °C, at pH 6.0-8.5 and with 0.5-1.0 % NaCl. The major fatty acids (>10 %) were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The known polar lipids comprised of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine. The isoprenoid quinone was Q-8. The G+C content of genomic DNA was 70.7 mol%. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the strain forms a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Aquabacterium in the class Betaproteobacteria. The most closely related phylogenetic neighbours were Aquabacterium limnoticumABP-4^T (97.8 % 16S rRNA gene sequence identity) and Aquabacterium communeB8^T (97.2 % 16SrRNA gene sequence identity). DNA-DNA relatedness values between YIM 730274^T and A. limnoticum KCTC 23306^T (46.4±0.4 %) and A. commune DSM 11901^T (42.2±1.2 %) were well below the 70 % limit for species identification. YIM 730274^T was distinguishable from other members of the genus Aquabacterium by the differences in phenotypic, chemotaxonomic and genotypic characteristics. YIM 730274^T merits recognition as a representative of a novel species of the genus Aquabacterium. It is proposed that the isolate should be classified in the genus Aquabacterium as representing a novel species, Aquabacteriumtepidiphilum sp. nov. The type strain is YIM 730274^T (=KCTC 52716^T=CCTCC AB 2016295^T).

Current taxonomy of Rhodococcus species and their role in infections

Rhodococcus is a genus of obligate aerobic, Gram-positive, partially acid-fast, catalase-positive, non-motile, and none-endospore bacteria. The genus Rhodococcus was first introduced by Zopf. This bacterium can be isolated from various sources of the environment and can grow well in non-selective medium. A large number of phenotypic characterizations are used to compare different species of the genus Rhodococcus, and these tests are not suitable for accurate identification at the genus and species level. Among nucleic acid-based methods, the most powerful target gene for revealing reliable phylogenetic relationships is 16S ribosomal RNA gene (16S rRNA gene) sequence analysis, but this gene is unable to differentiation some of Rhodococcus species. To date, whole genome sequencing analysis has solved taxonomic complexities in this genus. Rhodococcus equi is the major cause of foal pneumonia, and its implication in human health is related to cases in immunocompromised patients. Macrolide family together with rifampicin is one of the most effective antibiotic agents for treatment rhodococcal infections.

Actinoplanes deserti sp. nov., isolated from a desert soil sample

A novel actinomycete, designated strain YIM CF22^T, was isolated from a desert soil sample collected from Turpan in Xinjiang Uyghur Autonomous Region, north-western China. The taxonomic position of the strain YIM CF22^T is described based on a polyphasic approach. Strain YIM CF22^T was found to form irregular sporangia on agar media. It contains meso-diaminopimelic acid in the cell wall peptidoglycan. The major menaquinone was identified as MK-9(H₄); the polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, two unidentified phospholipids and two unidentified glycolipids. The whole cell sugars were found to be ribose, mannose, galactose, glucose and xylose. The major cellular fatty acids were found to be (> 5%) iso-C_16:0 (43.5%), anteiso-C_17:0 (10.2%), iso-C_15:0 (7.1%), C_17:1 ω8c (6.3%) and iso H-C_16:1 (5.9%). The G+C content was determined to be 70.8%. 16S rRNA gene sequence analysis of strain YIM CF22^T showed high similarity (97.0%) to Actinoplanes rishiriensis NBRC 108556^T. The strain also showed high 16S rRNA gene sequence similarities to Verrucosispora sediminis CGMCC 4.3550^T (96.9%) and Micromonospora tulbaghiae DSM 45142^T (96.8%). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM CF22^T clusters with A. rishiriensis NBRC 108556^T, Actinoplanes globisporus JCM 3186^T and Actinoplanes rhizophilus NEAU-A-2^T. Based on the differential phenotypic characteristics and the results of DNA-DNA relatedness and phylogenetic analysis, it is proposed that strain YIM CF22^T represents a novel species of the genus Actinoplanes, for which the name Actinoplanes deserti sp. nov. is proposed. The type strain is YIM CF22^T (= KCTC 39543^T = CCTCC AB2018113^T).

Phenylobacterium deserti sp. nov., isolated from desert soil

A novel bacterial strain, designated YIM 73061T, was isolated from the Cholistan desert in Punjab, Pakistan, and characterized by using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis revealed the highest levels of sequence similarity with respect to Phenylobacterium conjunctum FWC21T (97.6 %), Phenylobacterium lituiforme FaiI3T (97.4 %), Phenylobacteriumcomposti 4T-6T (97.0 %) and Phenylobacterium aquaticum W2-3-4T (96.8 %). Cells were Gram-stain-negative, aerobic and motile rods that formed orange colonies. The strain was oxidase- and catalase-positive. Growth occurred at 20-40 °C (optimum, 30-37 °C) at pH 5.0-8.0 (optimum, pH 7.0) and with 0-1 % (w/v) NaCl (optimum, 0-0.5 %). The major cellular fatty acids (>10 %) were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The polar lipid profile consisted of phosphatidylglycerol and four unidentified glycolipids. The major isoprenoid quinone was ubiquinone-10 (Q-10). The G+C content of the genomic DNA was 66.8 mol%. Strain YIM 73061T showed low levels of DNA-DNA relatedness to P. conjunctum FWC21T (27.2±2.6 %), P. lituiforme FaiI3T (24.6±1.1 %) and P.composti 4T-6T (18.4±3.1 %). On the basis of phylogenetic inference, chemotaxonomic characteristics and phenotypic data, strain YIM 73061T should be classified as representing a novel species, for which the name Phenylobacterium deserti sp. nov. is proposed. The type strain is YIM 73061T (=DSM 103871T=CCTCC AB 2016297T).

Nonomuraea cavernae sp. nov., a novel actinobacterium isolated from a karst cave sample

A novel actinobacterial strain, designated SYSU K10005^T, was isolated from a soil sample collected from a karst cave in Xingyi county, Guizhou province, south-west China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were aerobic and Gram-stain-positive. On the basis of 16S rRNA gene sequence analysis, strain SYSU K10005^T was most closely related to the type strains of the genus Nonomuraea, and shared highest sequence similarity of 98.4 % with Nonomuraea candida HMC10^T. DNA-DNA hybridization values between the two strains were less than 70 %. The whole-cell hydrolysates of strain SYSU K10005^T contained meso-diaminopimelic acid (diagnostic diamino acid), and arabinose, madurose and rhamnose (whole-cell sugars). The major isoprenoid quinone was MK-9(H4), while the major fatty acids were iso-C16 : 0, 10-methyl C17 : 0, C17 : 1ω8c and C17 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxyl-phosphatidylethanolamine, lyso-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides, an unidentified lipid, two unidentified ninhydrin-positive phosphoglycolipids and two unidentified phospholipids. The genomic DNA G+C content of strain SYSU K10005^T was 64.2 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K10005^T can be characterized to represent a novel species of the genus Nonomuraea, for which the name Nonomuraea cavernae sp. nov. is proposed. The type strain is SYSU K10005^T (=KCTC 39805^T=CGMCC 4.7368^T).

Nocardioides thalensis sp. nov., isolated from a desert

A novel actinobacterial strain, designated NCCP-696T, was isolated from the Thal desert in Punjab, Pakistan, and characterized by using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain NCCP-696T belongs to the genus Nocardioides and showed the highest level of sequence similarity with respect to Nocardioides panacisoliGsoil 346T (98.2 %) and less than 96.4 % to the strains of other species of the genus Nocardioides. Cells of strain NCCP-696T were Gram-positive, aerobic, non-motile rods and formed cream-coloured colonies. The strain was positive for oxidase and catalase. Growth occurred at 20-42 °C (optimum 30-37 °C) at pH 5.5-9.0 (optimum pH 7.0) and with 0-4 % NaCl (optimum 0-2 %, w/v). Strain NCCP-696T contained Iso-C16 : 0, C18 : 1ω9c, C17 : 1ω8c and C17 : 0 as the predominant fatty acids and was found to have LL-2,6-diaminopimelic acid in the cell-wall peptidoglycan. The polar lipid profile consisted of phosphatidylinositol, phosphatidylglycerol and one unknown phospholipid. The major menaquinone was MK-8(H4) (98.7 %) while a minor amount (1.3 %) of MK-9(H2) was also detected. The DNA G+C content of the genomic DNA was 71.6 mol%. The DNA-DNA hybridization value of the isolate against the closely related type strain Nocardioides panacisoliGsoil 346T was 56.3±1.4. On the basis of the phylogenetic inference, chemotaxonomic characteristics and phenotypic data, strain NCCP-696T should be classified as a novel species, for which the name Nocardioides thalensis sp. nov. is proposed. The type strain is NCCP-696T (=DSM 103833T=CCTCC AB 2016296T).

Sphingobacteriumsoli sp. nov., isolated from soil

A Gram-stain-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated YIM X0211T, was isolated from a soil sample of Shiling County, Yunnan Province, south-west China. The new isolate was characterized taxonomically by using a polyphasic approach. The strain grew optimally at 30 °C, at pH 7.0 and with 0-3 % (w/v) NaCl. It was positive for catalase and oxidase but negative for H2S production. Comparative 16S rRNA gene sequence analysis showed that strain YIM X0211T fell within the cluster comprising Sphingobacterium species and clustered with Sphingobacterium mizutaii DSM 11724T (97.93 % similarity). The G+C content of the genomic DNA was 41.2 mol%. The predominant respiratory quinone was menaquinone MK-7. The major fatty acids were iso-C15 : 0 2-OH, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). The polar lipids consisted of phosphatidylethanolamine, sphingolipid, and several unknown phospholipids or lipids. The DNA-DNA hybridization value between strain YIM X0211T and S. mizutaii DSM 11724T was 42.3±0.4 %, which is below the 70 % limit for species delineation. These chemotaxonomic data supported the affiliation of strain YIM X0211T to the genus Sphingobacterium. Based on the recorded phenotypic and genotypic characteristics, it is determined that the isolate represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium soli sp. nov. is proposed. The type strain is YIM X0211T (=KCTC 42696T=CGMCC 1.15966T).

Lentzea cavernae sp. nov., an actinobacterium isolated from a karst cave sample, and emended description of the genus Lentzea

A novel actinobacterial strain, designated SYSU K10001T, was isolated from a limestone sample collected from a karst cave in Xingyi county, Guizhou province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were aerobic and Gram-stain-positive. On the basis of 16S rRNA gene sequence analysis, strain SYSU K10001T was most closely related to the type strains of the genus Lentzea, Lentzea albida NBRC 16102T (98.8 % similarity) and Lentzea waywayandensis NRRL B-16159T (98.6 %), and is therefore considered to represent a member of the genus Lentzea. DNA-DNA hybridization values between strain SYSU K10001T and related type strains of the genus Lentzea were less than 70 %. In addition, meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell sugars were arabinose, fructose, mannose and xylose. The major isoprenoid quinone was MK-9(H4), while the major fatty acids (>10 %) were iso-C16 : 0 and C14 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified phospholipid and one unidentified lipid. The genomic DNA G+C content of strain SYSU K10001T was 69.4 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K10001T represents a novel species of the genus Lentzea, for which the name Lentzea cavernae sp. nov. is proposed. The type strain is SYSU K10001T (=KCTC 39804T=CGMCC 4.7367T=NBRC 112394T).

Deinococcus malanensis sp. nov., isolated from radiation-polluted soil

A Gram-staining positive, non-spore forming, short rod-shaped and coccus-shaped, non-motile, pink-colored, gamma- and UV-resistant strain, designated T93^T was isolated from soil of Malan area in Xinjiang Uyghur Autonomous Region, Northwest China. The taxonomic position of the new isolate was determined using a polyphasic approach. Strain T93^T shared the highest 16 S rRNA gene sequence similarity with Deinococcus deserti VCD115^T (97.54%). The genomic DNA G+C content of the isolate T93^T was 61.7 mol%. The predominant menaquinone was MK-8, while the major cellular fatty acids were iso-C_16:0, C_15:1 ω6c, C_16:0, C_17:1 ω8c and Summed Feature 3 (comprising C_16:1 ω7c and/or C_16:1 ω6c). The major polar lipid profiles consisted of diphosphatidylglycerol and phosphatidylinositol mannoside. Based on the phenotypic and genotypic data, strain T93^T is considered to represent a novel species of the genus Deinococcus, for which the name Deinococcus malanensis sp. nov. is proposed. The type strain is T93^T (= KCTC 33563^T = JCM 30331^T).

Saccharothrix lopnurensis sp. nov., a filamentous actinomycete isolated from sediment of Lop Nur

A novel actinomycete strain, designated YIM LPA2h(T), was isolated from a sediment sample collected from Lop Nur, Xinjiang Uygur Autonomous Region, North-West China. The taxonomic position of strain YIM LPA2h(T) was investigated by a polyphasic approach. The morphological and chemotaxonomic properties of the isolate were in accordance with the members of the genus Saccharothrix. The 16S rRNA gene sequence of the strain showed highest similarities to Saccharothrix yanglingensis (98.6 %), Saccharothrix longispora (98.4 %) and Saccharothrix hoggarensis (98.3 %). However, the DNA-DNA hybridization values between the new isolate YIM LPA2h(T) and S. yanglingensis, S. longispora and S. hoggarensis were significantly below 70 %. Strain YIM LPA2h(T) was found to contain meso-diaminopimelic acid as diagnostic diamino acid. The major sugars in whole-cell hydrolysates were rhamnose, galactose, mannose, glucose and fructose. The major polar lipids were identified as phosphatidylethanolamine, phosphatidylhydroxylethanolamine, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The predominant respiratory menaquinones were MK-9 (H4) and MK-10 (H4). The major fatty acids were C17:1 ω8c (15 %), iso-C15:0 (12 %), anteiso-C15:0 (12 %) and summed feature 3 (C16:1 ω6c/C16:1 ω7c, 10 %). The genomic DNA G+C content of strain YIM LPA2h(T) was determined to be 75 mol %. The genotypic and phenotypic results suggest that strain YIM LPA2h(T) represents a novel species of the genus Saccharothrix, for which the name Saccharothrix lopnurensis sp. nov. is proposed. The type strain is YIM LPA2h(T) (=CGMCC 4.7246(T)=KCTC 39545(T)).

List of new names and new combinations previously effectively, but not validly, published

The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.