Flavobacterium acetivorans sp. nov. and Flavobacterium galactosidilyticum sp. nov., psychrotolerant flavobacteria isolated from cultivated fish.

Two yellow-coloured strains, F-29T and F-340T, were isolated from fish farms in Antalya and Mugla in 2015 and 2017 during surveillance studies. The 16S rRNA gene sequence analysis showed that both strains belong to the genus Flavobacterium. A polyphasic approach involving a comprehensive genome analysis was employed to ascertain the taxonomic provenance of the strains. The overall genome-relatedness indices of digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) between the strains and the other members of the genus Flavobacterium were found to be well below the established thresholds of 70 and 95 %, respectively. The whole-genome-based phylogenetic analysis revealed that strain F-29T is closely related to Flavobacterium granuli (dDDH 39.3 % and ANI 89.4 %), while strain F-340T has a close relationship with the type strain of Flavobacterium pygoscelis (dDDH 25.6 % and ANI 81.5 %). Both strains were psychrotolerant with an optimum growth temperature of 25 °C. The chemotaxonomic characteristics of the strains were typical of the genus Flavobacterium. Both strains had phosphatidylethanolamine, aminolipids and unidentified lipids in their polar lipid profile and MK-6 as the isoprenoid quinone. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The genome size of the strains was 3.5 Mb, while G+C contents were 35.3 mol% for strain F-29T and 33.4 mol% for strain F-340T. Overall, the characterizations confirmed that both strains are representatives of two novel species within the genus Flavobacterium, for which the names Flavobacterium acetivorans sp. nov. and Flavobacterium galactosidilyticum sp. nov. are proposed, with F-29T (JCM 34193T=KCTC 82253T) and F-340T (JCM 34203T=KCTC 82263T) as the type strains, respectively.

Comprehensive genome analysis of five novel flavobacteria: Flavobacterium piscisymbiosum sp. nov., Flavobacterium pisciphilum sp. nov., Flavobacterium flavipigmentatum sp. nov., Flavobacterium lipolyticum sp. nov. and Flavobacterium cupriresistens sp. nov.

Eight isolates were obtained through a study on culture-dependent bacteria from fish farms and identified as members of the genus Flavobacterium based on pairwise analysis of the 16S rRNA gene sequences. The highest pairwise identity values were calculated as 98.8 % for strain F-30 T and Flavobacterium bizetiae, 99.0 % for strain F-65 T and Flavobacterium branchiarum, 98.7 % for strain F-126 T and Flavobacterium tructae, 98.2 % for strain F-323 T and Flavobacterium cupreum while 99.7 % identity level was detected for strain F-70 T and Flavobacterium geliluteum. In addition, strains F-33, Fl-77, and F-70 T shared 100 % identical 16S rRNA genes, while strains F-323 T and Fl-318 showed 99.9 % identity. A polyphasic approach including comparative analysis of whole-genome data was employed to ascertain the taxonomic provenance of the strains. In addition to the morphological, physiological, biochemical and chemotaxonomic characteristics of the strains, the overall genome-relatedness indices of dDDH and ANI below the established thresholds confirmed the classification of the strains as five novel species within the genus Flavobacterium. The comprehensive genome analyses of the strains were also conducted to determine the biosynthetic gene clusters, virulence features and ecological distribution patterns. Based on the polyphasic characterisations, including comparative genome analyses, it is concluded that strains F-30 T, F-65 T, F-70 T, F126T and F-323 T represent five novel species within the genus Flavobacterium for which Flavobacterium piscisymbiosum sp. nov. F-30 T (=JCM 34194 T = KCTC 82254 T), Flavobacterium pisciphilum sp. nov. F-65 T (=JCM 34197 T = KCTC 82257 T), Flavobacterium flavipigmentatum sp. nov. F-70 T (Fl-33 = Fl-77 = JCM 34198 T = KCTC 82258 T), Flavobacterium lipolyticum sp. nov. F-126 T (JCM 34199 T = KCTC 82259 T) and Flavobacterium cupriresistens sp. nov. F-323 T (Fl-318 = JCM 34200 T = KCTC 82260 T), are proposed.

Genome-based classification of Streptomyces anatolicus sp. nov., an actinobacterium with antimicrobial and cytotoxic activities, and reclassification of Streptomyces nashvillensis as a later heterotypic synonym of Streptomyces tanashiensis.

During the course of isolating novel actinobacteria producing bioactive metabolites, strain BG9HT was obtained from an arid soil sample in Erzurum, Turkey. Pairwise sequence comparisons for 16S rRNA gene sequences showed the strain was a member of the genus Streptomyces and it shared the highest 16S rRNA gene sequence identity of 99.7% with Streptomyces huasconensis HST28T. Comparative genome analyses based on digital DNA-DNA hybridization and average nucleotide identity revealed that strain BG9HT represents a novel species within the genus Streptomyces. The polyphasic analysis also confirmed that the strain has typical characteristics of the genus Streptomyces. The strain has LL-diaminopimelic acid as diagnostic amino acid, and galactose, mannose and trace amounts of glucose and ribose as whole-cell sugars. Polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, unidentified aminolipids, phospholipids and lipids. Major isoprenoid quinones were MK-9(H6), MK-9(H4), and MK-9(H8). Its genome size is approximately 7.2 Mb with 71.2% G+C content. The methanolic extract of strain BG9HT showed antimicrobial and cytotoxic activities. Further genomic analyses of strain BG9HT confirmed its high potential to produce novel secondary metabolites. On the basis of phenotypic and phylogenetic analyses, strain BG9HT represents a novel species of the genus Streptomyces, for which Streptomyces anatolicus sp. nov. is proposed, and it holds high promise for novel biosynthetic metabolites of value to the biopharmaceutical industry. We also propose Streptomyces nashvillensis as a later heterotypic synonym of Streptomyces tanashiensis as a result obtained through analysis of overall genome relatedness indices.

Genomic insight into Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. isolated from farmed rainbow trout in Turkey.

Four strains, designated as C-2, C-17T, C-39T and Ch-15, were isolated from farmed rainbow trout samples showing clinical signs during an investigation for a fish-health screening study. The pairwise 16S rRNA gene sequence analysis showed that strain C-17T shared the highest identity level of 98.1 % with the type strain of Chryseobacterium piscium LMG 23089T while strains C-2, C-39T and Ch-15 were closely related to Chryseobacterium balustinum DSM 16775T with an identity level of 99.3 %. A polyphasic approach involving phenotypic, chemotaxonomic and genome-based analyses was employed to determine the taxonomic provenance of the strains. The overall genome relatedness indices including dDDH and ANI analyses confirmed that strains C-2, C-17T, C-39T and Ch-15 formed two novel species within the genus Chryseobacterium. Chemotaxonomic analyses showed that strains C-17T and C-39T have typical characteristics of the genus Chryseobacterium by having phosphatidylethanolamine in their polar lipid profile, MK-6 as only isoprenoid quinone and the presence of iso-C15:0 as major fatty acid. The genome size and G + C content of the strains ranged between 4.4 and 5.0 Mb and 33.5 - 33.6 %, respectively. Comprehensive genome analyses revealed that the strains have antimicrobial resistance genes, prophages and horizontally acquired genes in addition to secondary metabolite-coding gene clusters. In conclusion, based on the polyphasic analyses conducted on the present study, strains C-17T and C-39T are representatives of two novel species within the genus Chryseobacterium, for which the names Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. with the type strains C-17T (=JCM 34190T = KCTC 82250T) and C-39T (=JCM 34191T = KCTC 822251T), respectively, are proposed.

Antimicrobial, antibiofilm, and anticancer potential of silver nanoparticles synthesized using pigment-producing Micromonospora sp. SH121.

Silver nanoparticles (AgNPs) have gained interest as an alternative pharmaceutical agent because of antimicrobial resistance and drug toxicity. Considering the increasing request, eco-friendly, sustainable, and cost-effective synthesis of versatile AgNPs has become necessary. In this study, green-made AgNPs were successfully synthesized using Micromonospora sp. SH121 (Mm-AgNPs). Synthesis was verified by surface plasmon resonance (SPR) peak at 402 nm wavelength in the UV-Visible (UV-Vis) absorption spectrum. Scanning electron microscopy (SEM) analysis depicted that Mm-AgNPs were in the size range of 10-30 nm and spherical. Fourier transform infrared spectroscopy (FTIR) confirmed the existence of bioactive molecules on the surface of nanoparticles. The X-ray diffraction (XRD) analysis revealed the face-centered cubic (fcc) structure of the Mm-AgNPs. Their polydispersity index (PDI) and zeta potential were 0. 284 and -35.3 mV, respectively. Mm-AgNPs (4-32 µg/mL) exhibited strong antimicrobial activity against Bacillus cereus, Enterococcus faecalis, Enterococcus hirae, Escherichia coli, Klebsiella pneumoniae, Proteus vulgaris, Pseudomonas putida, Staphylococcus epidermidis, Streptococcus pneumoniae, and Aspergillus flavus. Mm-AgNPs partially inhibited the biofilm formation in Acinetobacter baumannii, E. coli, K. pneumoniae, and Pseudomonas aeruginosa. Furthermore, results showed that low concentrations of Mm-AgNPs (1 and 10 µg/mL) caused higher cytotoxicity and apoptosis in DU 145 cells than human fibroblast cells. Based on the results, Mm-AgNPs have an excellent potential for treating infectious diseases and prostate cancer.

Genomic insight into Myroides oncorhynchi sp. nov., a new member of the Myroides genus, isolated from the internal organ of rainbow trout (Oncorhynchus mykiss).

The strain M-43T was isolated from the Oncorhynchus mykiss from a fish farm in Mugla, Turkey. Pairwise 16S rRNA gene sequence analysis was used to identify strain M-43T. The strain was a member of the genus Myroides sharing the highest 16S rRNA gene sequence identity levels of 98.7%, 98.3%, and 98.3% with the type strains of M. profundi D25T, M. odoratimimus subsp. odoratimimus CCUG 39352T and M. odoratimimus subsp. xuanwuensis DSM27251T, respectively. A polyphasic taxonomic approach including whole genome-based analyses was employed to confirm the taxonomic provenance of strain M-43T within the genus Myroides. The overall genome relatedness indices (OGRI) for strain M-43T compared with its most closely related type strains M. odoratimimus subsp. xuanwuensis DSM 27251T, M. profundi D25T, and M. odoratimimus subsp. odoratimimus ATCC BAA-634T, were calculated as 25.3%, 25.1%, and 25% for digital DNA-DNA hybridization (dDDH), 83.3%, 83.6%, and 83.4% for average nucleotide identity (ANI) analyses, respectively. The OGRI values between strain M-43T and its close neighbors confirmed that the strain represents a novel species in the genus Myroides. The DNA G + C content of the strain is 33.7%. The major fatty acids are iso-C15:0 and summed feature 9 (iso-C17:1 ω9c and/or 10-methyl C16:0). The predominant polar lipids are phosphatidylethanolamine, an amino-lipid and five unidentified lipids. The major respiratory quinone is MK-6. Chemotaxonomic and phylogenomic analyses of this isolate confirmed that the strain represents a novel species for which the name Myroides oncorhynchi sp. nov. is proposed, with M-43T as the type strain (JCM 34205T = KCTC 82265T).

Shewanella oncorhynchi sp. nov., a novel member of the genus Shewanella, isolated from Rainbow Trout (Oncorhynchus mykiss).

A strain, S-1T was isolated from rainbow trout (Oncorhynchus mykiss) exhibiting clinical symptoms of lens atrophy, inappetence, visual impairment and growth retardation. The strain was identified as representing a member of the genus Shewanella on the basis of the results of 16S rRNA gene sequence analysis. The neighbor-joining phylogenetic tree based on 16S rRNA gene sequences indicated that S-1T clustered with Shewanella putrefaciens JCM 20190T, Shewanella profunda DSM 15900T, and Shewanella hafniensis P010T, sharing 99.3, 98.8 and 87.7% 16S rRNA gene similarities, respectively. A polyphasic taxonomic approach including phenotypic, chemotaxonomic, and genomic characterization was employed to ascertain the taxonomic position of S-1T within the genus Shewanella. The overall genome relatedness indices (OGRI) for S-1T compared with the most closely related type strains S. hafniensis ATCC BAA-1207T, Shewanella baltica NCTC 10735T, S. putrefaciens ATCC 8071T and S. profunda DSM 15900T were calculated as 40.8, 40.1, 28.5 and 27.3% for digital DNA-DNA hybridization (dDDH), and 91.6, 91.0, 86.3 and 85.1% for average nucleotide identity (ANI), respectively. OGRI values between S-1T and its close neighbours confirmed that the strain represents a novel species in the genus Shewanella.The DNA G+C content of the strain is 45.2%. Major fatty acids were C17 : 1ω8c, C15 : 0iso, and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The predominant polar lipids were phosphatidylethanolamine, phospholipid, amino-phospholipid and unidentified lipids. The major respiratory quinones were ubiquinone-8, ubiquinone-7 and menaquinone-7. Chemotaxonomic and phylogenomic analyses of this isolate confirmed that the strain represents a novel species for which the name Shewanella oncorhynchi sp. nov. is proposed, with S-1T as the type strain (JCM 34183T= KCTC 82249T).

Description of the two novel species of the genus Helicobacter: Helicobacter anatolicus sp. nov., and Helicobacter kayseriensis sp. nov., isolated from feces of urban wild birds.

A total of 26 Gram-negative, motile, gently curved, and rod-shaped isolates were recovered, during a study to determine the faeco-prevalence of Helicobacter spp. in urban wild birds. Pairwise comparisons of the 16S rRNA gene sequences indicated that these isolates belonged to the genus Helicobacter and phylogenetic analysis based on the 16S rRNA gene sequences showed that the isolates were separated into two divergent groups. The first group consisted of 20 urease-positive isolates sharing the highest 16S rRNA gene sequence identity levels of 98.5-98.6% to H. mustelae ATCC 43772T, while the second group contained six urease-negative isolates with the sequence identity level of 98.5% to the type strain of H. pametensis ATCC 51478T. Five isolates were chosen and subjected to comparative whole-genome analysis. The phylogenetic analysis of the 16S rRNA, gyrA and atpA gene sequences showed that Helicobacter isolates formed two separate phylogenetic clades, differentiating the isolates from the other Helicobacter species. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses between strains faydin-H8T, faydin-H23T and their close neighbors H. anseris MIT 04-9362T and H. pametensis ATCC 51478T, respectively, confirmed that both strains represent novel species in the genus Helicobacter. The DNA G+C contents of the strains faydin-H8T and faydin-H23T are 32.0% and 37.6%, respectively. The results obtained for the characterization of the wild bird isolates indicate that they represent two novel species, for which the names Helicobacter anatolicus sp. nov., and Helicobacter kayseriensis sp. nov., are proposed, with faydin-H8T(=LMG 32237T = DSM 112312T) and faydin-H23T(=LMG 32236T = CECT 30508T) as respective type strains.

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

Exploration of unexplored habitats for novel actinobacteria with high bioactivity potential holds great promise in the search for novel entities. During the course of isolation of actinobacteria from desert soils, four actinobacteria, designated as 5K548T, 7K502T, 16K309T and 16K404T, were isolated from the Karakum Desert and their bioactivity potential as well as taxonomic provenances were revealed by comprehensive genome analyses. Pairwise sequence analyses of the 16S rRNA genes indicated that the four strains are representatives of putatively novel taxa within the prolific actinobacterial genus Saccharopolyspora. The strains have typical chemotaxonomic characteristics of the genus Saccharopolyspora by having meso-diaminopimelic acid as diagnostic diaminoacid, arabinose, galactose and ribose as whole-cell sugars. Consistent with this assignment, all of the isolates contained phosphatidylcholine in their polar lipid profiles and MK-9(H4) as the predominant menaquinone. The sizes of the genomes of the isolates ranged from 6.0 to 10.2 Mb and the associated G + C contents from 69.6 to 69.7 %. Polyphasic characterizations including determination of overall genome relatedness indices revealed that the strains are representatives of four novel species in the genus Saccharopolyspora. Consequently, isolates 5K548T, 7K502T, 16K404T and 16K309T are proposed as novel Saccharopolyspora species for which the names of Saccharopolyspora karakumensis sp. nov., Saccharopolyspora elongata sp. nov., Saccharopolyspora aridisoli sp. nov. and Saccharopolyspora terrae sp. nov. are proposed, respectively. Comprehensive genome analysis for biosynthetic gene clusters showed that the strains have high potential for novel secondary metabolites. Moreover, the strains harbour many antimicrobial resistance genes providing more evidence for their potentiality for bioactive metabolites.

Comprehensive genome analysis of a novel actinobacterium with high potential for biotechnological applications, Nonomuraea aridisoli sp. nov., isolated from desert soil.

During a study to isolate such actinobacteria with unique metabolic potential, a novel actinobacterium, designated KC333T, was isolated from a soil sample collected from the Karakum Desert, Turkmenistan. The taxonomic position of the strain was investigated using a polyphasic approach. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain was most closely related to Nonomuraea terrae CH32T (99.0% sequence similarity), Nonomuraea maritima FXJ7.203 T (98.9%), Nonomuraea candida HMC10T (98.7%) and Nonomuraea gerenzanensis ATCC 39727 T (98.6%), and is therefore considered to represent a member of the genus Nonomuraea. However, the average nucleotide identity and digital DNA-DNA hybridization based on whole-genome sequences between strain KC333T and close relatives demonstrated that it represents a novel species of the genus Nonomuraea. The major cellular fatty acids of strain KC333T were iso-C16: 0, C17:0 10-methyl and iso-C16: 0 2OH. Strain KC333T contained meso-diaminopimelic, mannose, madurose and ribose in the cell-wall peptidoglycan. The predominant menaquinones were MK-9(H4) and MK-9(H6). The genome size of strain KC333T is approximately 9.86 Mb, and the genomic DNA G + C content of the strain is 71.3%. In addition to the polyphasic characterisation, comprehensive genome analysis for gene clusters encoding carbohydrate-active enzymes and bioactive secondary metabolites as well as CRISPR-associated sequences revealed the high biotechnological potential of the strain. Based on evidence collected from the genotypic, phenotypic, and phylogenetic analyses, a novel species, Nonomuraea aridisoli sp. nov. is proposed with KC333T (= DSM 107062 T = JCM 32584 T = KCTC 49111 T) as the type strain.

Flavobacterium muglaense sp. nov. isolated from internal organs of apparently healthy rainbow trout.

Two yellow-pigmented isolates, F-60T and F-392, were isolated from the internal organs of an apparently healthy rainbow trout (Oncorhynchus mykiss). The strains were identified as members of the genus Flavobacterium based on the results of 16S rRNA gene sequence analysis. Strains F-60T and F-392 had the highest 16S rRNA gene sequence identity level of 97.4 % to the type strain of Flavobacterium crassostreae LPB0076T. A polyphasic taxonomic approach including phenotypic, chemotaxonomic and genomic characterization was employed to ascertain the taxonomic position of the strains within the genus Flavobacterium. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity based on blast (ANIb) values for strains F-60T and F-392 were calculated as 100 %. However, dDDH and ANI analyses between the strains and their close neighbours confirmed that both strains represent a novel species in the genus Flavobacterium. The strains shared the highest dDDH and ANIb levels of 23.3 and 77.9%, respectively, with the type strain of Flavobacterium frigidarium DSM 17623T while those values for F. crassostreae LPB0076T were obtained as 21.4-21.5 % and 76.3 %. The DNA G+C content of the strains was 34.5 mol%. Chemotaxonomic and phylogenomic analyses of these isolates confirmed that both strains are representatives of a novel species for which the name Flavobacterium muglaense sp. nov. is proposed, with F-60T as the type strain (=JCM 34196T=KCTC 82256T).

Cloning, expression, biochemical characterization, and molecular docking studies of a novel glucose tolerant ß-glucosidase from Saccharomonospora sp. NB11.

Most of the presently known ß-glucosidases are sensitive to end-product inhibition by glucose, restricting their potential use in many industrial applications. Identification of novel glucose tolerant ß-glucosidase can prove a pivotal solution to eliminate end-product inhibition and enhance the overall lignocellulosic saccharification process. In this study, a novel gene encoding ß-glucosidase BglNB11 of 1405bp was identified in the genome of Saccharomonospora sp. NB11 and was successfully cloned and heterologously expressed in E. coli BL21 (DE3).The presence of conserved amino acids; NEPW and TENG indicated that BglNB11 belonged to GH1 ß-glucosidases. The recombinant enzyme was purified using a Ni-NTA column, with the molecular mass of 51 kDa, using SDS-PAGE analysis. BglNB11 showed optimum activity at 40 °C and pH 7 and did not require any tested co-factors for activation. The kinetic values, Km, Vmax, kcat, and kcat/Km of purified enzyme were 0.4037 mM, 5735.8 µmol/min/mg, 5042.16 s-1 and 12487.71 s-1 mM-1, respectively. The enzyme was not inhibited by glucose to a concentration of 4 M but was slightly stimulated in the presence of glucose. Molecular docking of BglNB11 with glucose suggested that the relative binding position of glucose in the active site channel might be responsible for modulating end product tolerance and stimulation. ß-glucosidase from BglNB11 is an excellent enzyme with high catalytic efficiency and enhanced glucose tolerance compared to many known glucose tolerant ß-glucosidases. These unique properties of BglNB11 make it a prime candidate to be utilized in many biotechnological applications.

Flavobacterium turcicum sp. nov. and Flavobacterium kayseriense sp. nov. isolated from farmed rainbow trout in Turkey.

During a study on culturable microorganisms from fish farms, four yellow-pigmented gram negative, rod shaped isolates, F-47T, F-339T, F-380 and F-400, were recovered from rainbow trout samples exhibiting clinical signs. Based on 16S rRNA gene sequence analysis, the strains were identified as members of the genus Flavobacterium. Strains F-47T and F-380 shared the highest 16S rRNA gene sequence identity level of 97.6% with the type strain of Flavobacterium frigoris DSM 15719T while strains F-339T and F-400 shared the highest identity level of 97.6% with the type strain of F. caseinilyticum AT-3-2T. A polyphasic taxonomic approach including phenotypic and genomic characterization as well as whole-cell MALDI-TOF mass spectrometry analyses was employed to ascertain the taxonomic position of the strains within the genus Flavobacterium. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses between strains F-47T, F-339T and their close neighbours F. frigoris DSM 15719T and F. caseinilyticum AT-3-2T, respectively, confirmed that both strains represent novel species in the genus Flavobacterium. The DNA G+C contents of the strains F-47T and F-339T are 34.3% and 35.3%, respectively. It can be concluded on the basis of polyphasic characterization as well as pairwise genome comparisons that the strains F-47T and F-339T represent two novel species within the genus Flavobacterium, for which Flavobacterium kayseriense sp. nov. F-47T (=JCM 34195T=KCTC 82255T) and Flavobacterium turcicum sp. nov. F-339T (=JCM 34202T=KCTC 82262T) are proposed, respectively.

Genomic insight into a novel actinobacterium, Actinomadura rubrisoli sp. nov., reveals high potential for bioactive metabolites.

Isolation of novel actinobacteria from unexplored habitats as potential sources of novel drug leads has utmost importance. During the course of screening arid soil samples for novel actinobacteria, strain H3C3T was isolated from Malatya, Turkey and its taxonomic position was revealed by a genome-based polyphasic approach. Pairwise sequence comparison of the 16S rRNA gene showed that the strain is closely related to Actinomadura fibrosa JCM 9371T with sequence identity level of 99.0%. Comparative genome analyses based on digital DNA-DNA hybridization and average nucleotide identity indicated that strain H3C3T represents a novel species within the genus Actinomadura. The strain has typical characteristics of the genus Actinomadura, i.e. meso-diaminopimelic acid as diagnostic amino acid; galactose, glucose, madurose and ribose as whole-cell sugars. Major menaquinones detected were MK-9(H6), MK-9(H8) and polar lipids were diphosphatidylglycerol, phosphatidylinositol, glycophospholipid and unknown phospholipid and lipids. Its genome size is approximately 10.2 Mb with G+C content of 71.6%. Further genomic analyses of strain H3C3T indicated its high potential for novel biosynthetic gene clusters coding for various chemical structures. On the basis of phenotypic and phylogenetic analyses, strain H3C3T represents a novel species of the genus Actinomadura, for which Actinomadura rubrisoli sp. nov. is proposed, and it holds high promise for novel biosynthetic metabolites of value to biopharmaceutical industry.

Genome-based classification of Calidifontibacillus erzurumensis gen. nov., sp. nov., isolated from a hot spring in Turkey, with reclassification of Bacillus azotoformans as Calidifontibacillus azotoformans comb. nov. and Bacillus oryziterrae as Calidifontibacillus oryziterrae comb. nov.

A novel Gram-stain-positive, rod-shaped, endospore-forming, motile, aerobic bacterium, designated as P2T, was isolated from a hot spring water sample collected from Ilica-Erzurum, Turkey. Phylogenetic analyses based on 16S rRNA gene sequence comparisons affiliated strain P2T with the genus Bacillus, and the strain showed the highest sequence identity to Bacillus azotoformans NBRC 15712T (96.7 %). However, the pairwise sequence comparisons of the 16S rRNA genes revealed that strain P2T shared only 94.7 % sequence identity with Bacillus subtilis subsp. subtilis NCIB 3610T, indicating that strain P2T might not be a member of the genus Bacillus. The digital DNA-DNA hybridization and average nucleotide identity values between strain P2T and B. azotoformans NBRC 15712T were 19.8 and 74.2 %, respectively. The cell-wall peptidoglycan of strain P2T contained meso-diaminopimelic acid. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an aminophospholipid, five unidentified phospholipids and two unidentified lipids while the predominant isoprenoid quinone was MK-7. The major fatty acids were iso-C15 : 0 and iso-C16 : 0. The draft genome of strain P2T was composed of 82 contigs and found to be 3.5 Mb with 36.1 mol% G+C content. The results of phylogenomic and phenotypic analyses revealed that strain P2T represents a novel genus in the family Bacillaceae, for which the name Calidifontibacillus erzurumensis gen. nov., sp. nov. is proposed. The type strain of Calidifontibacillus erzurumensis is P2T (=CECT 9886T=DSM 107530T=NCCB 100675T). Based on the results of the present study, it is also suggested that Bacillus azotoformans and Bacillus oryziterrae should be transferred to this novel genus as Calidifontibacillus azotoformans comb. nov. and Calidifontibacillus oryziterrae comb. nov., respectively.

Bacillus pasinlerensis sp. nov., a thermophilic bacterium isolated from a hot spring in Turkey.

A Gram-reaction-positive, endospore-forming bacterium, designated strain P1T, was isolated from water samples collected from Pasinler Hot Spring and characterized using a polyphasic approach to clarify its taxonomic position. Strain P1T was found to have chemotaxonomic and morphological characteristics consistent with its classification in the genus Bacillus. The strain shared the highest 16S rRNA gene sequence identity values with Bacillus thermolactis R-6488T (97.6 %) and Bacillus kokeshiiformis MO-04T (97.2 %) and formed a distinct clade with both type strains in the phylogenetic trees based on 16S rRNA gene sequences. Strain P1T could grow optimally at 55 °C and in the presence of 2 % NaCl. The organism was found to contain meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The predominant menaquinone was determined to be MK-7. The major cellular fatty acids were identified as iso-C15 : 0, iso-C17 : 0 and anteiso-C17 : 0. Based upon the consensus of phenotypic and phylogenetic analyses, strain P1T represents a novel species of the genus Bacillus, for which the name Bacillus pasinlerensis sp. nov. is proposed. The type strain is P1T (=DSM 107529T=CECT 9885T=NCCB 100674T).

Nonomuraea terrae sp. nov., isolated from arid soil.

During the course of isolating rare actinobacteria from unexplored habitats, strain CH32T was obtained from an arid soil sample in eastern Anatolia, Turkey. Polyphasic characterization and comprehensive genome analyses showed that the strain is a member of the genus Nonomuraea and it is closely related to Nonomuraea gerenzanensis ATCC 39727T, Nonomuraea polychroma DSM 43925T and Nonomuraea maritima FXJ7.203T with gene identity level of 98.7%, 98.2% and 98.1%, respectively. The whole-cell hydrolysates contain meso-diaminopimelic acid as diagnostic diaminoacid and glucose, ribose, galactose, mannose and madurose as whole cell sugars. The predominant menaquinones are MK-9(H4), MK-9(H6) and MK-9(H2) while MK-9 exists as minor component. The polar lipid profile consists of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, glycolipid, glycophospholipids, phospholipids and unidentified lipids. The major cellular fatty acids are iso-C16:0 and C17:0 10-methyl. The total genome size is about 9.6 Mb and the G + C content is 71.0%. The genome contains biosynthetic gene clusters encoding for terpenes, siderophores, a type III polyketide synthase, a non-ribosomal polypeptide synthetase and a bacteriocin. The genome-based comparisons of the strain with its phylogenetic neighbours, as indicated by digital DNA-DNA hybridization and average nucleotide identity analyses, reveal that strain CH32T (= JCM 33876T = KCTC 49368T) is a novel member of the genus Nonomuraea, for which Nonomuraea terrae sp. nov. is proposed.

Shimazuella alba sp. nov. isolated from desert soil and emended description of the genus Shimazuella Park et al. 2007.

A novel, Gram-stain-positive bacterium, designated KC615T, was isolated from desert soil which was collected from the Karakum Desert, Turkmenistan. Phylogenetic analysis based on an almost-complete 16S rRNA gene sequence showed that isolate KC615T formed a monophyletic clade with Shimazuella kribbensis KCTC 9933T, sharing 98.2% similarity and polyphasic taxonomic studies confirmed the affiliation of the strain to the genus Shimazuella. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Whole-cell hydrolysates contained ribose and glucose. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and hydroxy-phosphatidylethanolamine. The predominant menaquinones (> 10%) were MK-9(H4) and MK-10(H4). Major fatty acids were anteiso-C15:0, C20:0 and C18:0. The genomic DNA G + C content observed for strain KC615T was 38.5 mol%. Based on 16S rRNA gene similarity, DNA-DNA hybridization value, chemotaxonomic characteristics and differential physiological properties, strain KC615T is considered to represent a novel species within the genus Shimazuella, for which the name Shimazuella alba sp. nov. is proposed. The type strain is KC615T (= JCM 33532T = CGMCC 4.7616T).

Genome-based classification of three novel actinobacteria from the Karakum Desert: Jiangella asiatica sp. nov., Jiangella aurantiaca sp. nov. and Jiangella ureilytica sp. nov.

Three isolates, 5K138T, 8K307T and KC603T, with typical morphological characteristics of members of the genus Jiangella were obtained during a study searching for novel actinobacteria with biosynthetic potential from the Karakum Desert. A polyphasic approach was adopted to determine taxonomic affiliations of the strains. The strains showed chemotaxonomic properties consistent with their classification as representing members of the genus Jiangella such as ll-diaminopimelic acid in the cell wall peptidoglycan, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as major polar lipids as well as MK-9(H4) as a major menaquinone. Pairwise sequence comparisons of the 16S rRNA genes showed that the strains were closely related to Jiangella alba DSM 45237T, Jiangella rhizosphaerae NEAU-YY265T and Jiangella mangrovi 3SM4-07T with higher than 99 % sequence identities. However, a combination of phenotypic and phylogenetic approaches as well as genome-based comparative analyses confirmed the taxonomic positions of these strains as representing distinct species within the genus Jiangella. Therefore, strains 5K138T, 8K307T and KC603T should each be classified as representing a novel species within the genus Jiangella, for which the names Jiangella asiatica sp. nov., Jiangella aurantiaca sp. nov. and Jiangella ureilytica sp. nov. are proposed, respectively. The type strains of the proposed novel species are as follows: Jiangella asiatica 5K138T (=JCM 33518T=CGMCC 4.7672T), Jiangella aurantiaca 8K307T (=JCM 33519T=CGMCC 4.7621T) and Jiangella ureilytica KC603T (=JCM 33520T=CGMCC 4.7618T).