Hybridization Values Research Articles

Neptunitalea lumnitzerae sp. nov. isolated from the phyllosphere of the mangrove Lumnitzera racemosa Willd.

A Gram-stain-negative, rod-shaped, non-motile, aerobic, light-yellow-pigmented bacterium, designated as strain Y10T, was isolated from Lumnitzera racemosa leaf in Iriomote island mangrove forests in Japan. The 16S rRNA gene sequence analysis revealed that the isolate Y10T was affiliated with the family Flavobacteriaceae, and the sequence showed the highest sequence identity to that of Neptunitalea chrysea NBRC 110019T (97.2%)and others with below 96% sequence identity. The draft genome analysis revealed that its genomic size is 3.85 Mbp with G + C content 34.1%. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between strain Y10T and Neptunitalea chrysea NBRC 110019T was 79.07%, 76.35% and 19.6%, respectively, which were below the thresholds for prokaryotic species delineation (95-96%, 85%, and 70%, respectively). MK-6 was the only menaquinone, and the major cellular fatty acids (> 10% of the total fatty acids) were iso-C15:0, iso-C17:0 3-OH, and summed feature 3 (comprised of C16:1ω7c-iso and C15:0 2-OH). Based on its distinct phylogenetic position and genotypic and phenotypic characteristics, the strain represents a novel species of the genus Neptunitalea, for which the name Neptunitalea lumnitzerae sp. nov. is proposed. The type strain is Y10T (= DSM 110280T = NBRC 115783T).

Halobellus marinus sp. nov., Halobellus ordinarius sp. nov., Halobaculum rarum sp. nov., and Halorarum halobium sp. nov., halophilic archaea isolated from marine solar salt and a saline lake.

Four halophilic archaeal strains were isolated from sea salt and a saline lake in China. Based on phylogenetic and phylogenomic analyses, the four strains are related to the genera of Halobellus, Halobaculum, and Halorarum within the family Haloferacaceae. The four strains possess genes responsible for carotenoid synthesis, maintenance of a high internal salt concentration, as well as diverse enzymes with biotechnological potential. The average nucleotide identity (ANI), average amino acid identity (AAI), and digitalDNA-DNA hybridization (dDDH) values among these four strains and their related species were lower than the established thresholds proposed for species demarcation. Strains DFY28T, ZY16T, QDC11T, and XH14T were distinguished from related species based on a variety of phenotypic characteristics. The major polar lipids of these four strains were similar to those of respective relatives within the genera Halobellus, Halobaculum, and Halorarum. The phenotypic, phylogenetic, and genome-based analyses suggest that strains DFY28T (= CGMCC 1.17470T = JCM 34310T), ZY16T (= CGMCC 1.17476T = JCM 34311T), QDC11T (= MCCC 4K00127T = KCTC 4308T), and XH14T (= CGMCC 1.17028T = JCM 34145T) represent four novel species of the genera Halobellus, Halobaculum and Halorarum, for which the names Halobellus marinus sp. nov., Halobellus ordinarius sp. nov., Halobaculum rarum sp. nov., and Halorarum halobium sp. nov. are proposed.

Paludibacillus litoralis gen. nov., sp. nov.: a novel species of a novel genus in the family Paracoccaceae, isolated from the sediment of a tidal flat located in Zhoushan, China.

A Gram-stain-negative, aerobic and rod-shaped bacterium, designated as HZG-20T, was isolated from a tidal flat in Zhoushan, Zhejiang Province, China. The 16S rRNA sequence similarities between strain HZG-20T and Pikeienuella piscinae RR4-56T, Coraliihabitans acroporae NNCM2T, Parvibaculum indicum P31T and Zhengella mangrovi X9-2-2T were 98.9, 91.7, 91.0 and 91.0%, respectively. Colonies of strain HZG-20T were 1.4 mm in diameter, milky white, round, smooth and convex after cultivating on marine agar at 30 °C for 48 h. Cells were catalase and oxidase-negative. Growth occurred at 15-37 ℃ (optimum, 28 ℃), pH 5.0-9.0 (optimum, pH 6.0-8.0) and with 0-8% (w/v) NaCl (optimum, 1-3%). It contained Menaquinone-8 (H2) as the sole respiratory quinone, and C16:0 (11.8-13.6%), C18:1 ω9c (6.8-13.3%) and C15:0 anteiso (10.9-27.7%) as the major cellular fatty acids. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid, one unidentified phosphoglycolipid, two unidentified glycolipids (GL1-GL2) and three unidentified lipids (L1-L3). The genome of strain HZG-20T was 3 835 886 bp in length, comprised 3746 protein-coding genes, with DNA G+C content of 67.1 mol%. The phylogenetic and phylogenomic trees indicated that strain HZG-20T formed an independent and stable clade with P. piscinae RR4-56T. However, the average nucleotide identity, digit DNA-DNA hybridization and average amino acid identity values between strain HZG-20T and P. piscinae RR4-56T, C. acroporae NNCM2T, P. indicum P31T and Z. mangrovi X9-2-2T were 81.6, 71.1, 68.7 and 69.5%; 23.0, 18.5, 17.9 and 17.5%; and 78.2, 56.8, 56.5 and 61.9%, respectively, together with distinct chemotaxonomic features, indicating strain HZG-20T should not be assigned to known genera. As a result, a novel species of a novel genus within the family Paracoccaceae, designated as Paludibacillus litoralis gen. nov., sp. nov., was proposed. The type strain is HZG-20T (MCCC 1K08468T=KCTC 82692T).

Reclassification of Salinisphaera halophila Zhang et al. 2012 as a Later Heterotypic Synonym of Salinisphaera orenii Park et al. 2012.

In the present study, the taxonomic position of Salinisphaera halophila (NZ_AYKF00000000)and Salinisphaera orenii (NZ_AYKH00000000)was re-evaluated. In addition, their metabolic potentials and mechanisms for mitigating stress conditions were determined. Comparisons of 16S rRNA gene sequences, analysis of the phylogenetic tree, phylogenomic tree, average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH) values were conducted. The 16S rRNA gene sequence similarity between Salinisphaera halophila YIM 95161Tand Salinisphaera orenii MK-B5Twas 100%. In phylogenetic and phylogenomic trees, Salinisphaera halophila YIM 95161Tand Salinisphaera orenii MK-B5Tclustered together. Both species encode genes for glycolysis, citrate cycle, pentose phosphate pathway, Entner-Doudoroff pathway, nitrate assimilation, and assimilatory sulfate reduction. They employ salt-in and salt-out strategies to mitigate salt stress. The ANI and dDDH values between Salinisphaera halophila YIM 95161Tand Salinisphaera orenii MK-B5Twere 96.6 and 72.1%, respectively, above the cut-off (95-96% for ANI and 70% for dDDH) for species delineation. Based on the above results, we propose to reclassify Salinisphaera halophila Zhang et al. 2012 as a later heterotypic synonym of Salinisphaera orenii Park et al. 2012.

Reclassification of Salisediminibacterium haloalkalitolerans Sultanpuram et al. 2015 as a Later Heterotypic Synonym of Salisediminibacterium halotolerans Jiang et al. 2012.

In the present study, the taxonomic position of Salisediminibacterium haloalkalitolerans was evaluated by determining the 16S rRNA gene sequence similarity, genome relatedness, and phylogenetic analyses. The 16S rRNA gene sequences extracted from the genomes of Salisediminibacterium haloalkalitolerans 10nlgT and Salisediminibacterium halotolerans DSM 26530T showed 100% similarity, supporting their classification as the same species. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between S. haloalkalitolerans and S. halotolerans were 97.7 and 80.2%, respectively, above the cutoff value (95-96% ANI; 70% dDDH) for species delineation. S. haloalkalitolerans and S. halotolerans should be classified as the same species because the 16S rRNA gene phylogeny and phylogenomic tree (based on 71 bacterial single-copy genes) showed no genetic divergence between them. Based on the above results and the rule of priority in nomenclature, we propose to reclassify Salisediminibacterium haloalkalitolerans Sultanpuram et al. 2015 as a later heterotypic synonym of Salisediminibacterium halotolerans Jiang et al. 2012.

Gallibacterium faecale sp. nov., Isolated from Dairy Cow Feces.

A facultative anaerobic, Gram-stain-negative, non-motile, rod-shaped bacterial strain AGMB14963T was isolated from the feces of a dairy cow. A 16S rRNA gene sequence-based phylogenetic analysis revealed that strain AGMB14963T belongs to the genus Gallibacterium, with Gallibacterium salpingitidis F150T being the closest species (95.8% 16S rRNA gene sequence similarity). Whole-genome sequence analysis revealed that strain AGMB14963T had a 37.0% G + C genomic DNA content and a genome size of 2.58Mb. In addition, the strain contained 53 tRNA and 2 rRNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strains AGMB14963T and G. salpingitidis F150T were 82.3 and 24.9%, respectively. Further, strain AGMB14963T was positive for oxidase and catalase, but negative for urease. Optimal growth of strain AGMB14963T occurred at 37 ℃, pH 8, and in 0.5% NaCl-containing medium. The predominant cellular fatty acids (> 10%) in strain AGMB14963T were C14:0, C16:0, and summed feature 3. Strain AGMB14963T produced lactic acid and isobutyric acid as the major end products of glucose fermentation. Polar lipids consisted of one phospholipid and one phosphoaminolipid. According to the genomic, physiologic, and chemotaxonomic characteristics, strain AGMB14963T represents a novel species of the genus Gallibacterium, for which the name Gallibacterium faecale sp. nov. is proposed. The type strain is AGMB14963T (= KCTC 25487T = NBRC 116419T).

Comparative Genomics Reveals Evidence of the Genome Reduction and Metabolic Potentials of Aliineobacillus hadale Isolated from Challenger Deep Sediment of the Mariana Trench.

Hadal zones account for the deepest 45% of oceanic depth range and play an important role in ocean biogeochemical cycles. As the least-explored aquatic habitat on earth, further investigation is still required to fully elucidate the microbial taxonomy, ecological significance, metabolic diversity, and adaptation in hadal environments. In this study, a novel strain Lsc_1132T was isolated from sediment of the Mariana Trench at 10,954 m in depth. Strain Lsc_1132T contains heterogenous 16S rRNA genes, exhibiting the highest sequence similarities to the type strains of Neobacillus drentensis LMG 21831T, Neobacillus dielmonensis, Neobacillus drentensis NBRC 102427T, Neobacillus rhizosphaerae, and Neobacillus soli NBRC 102451T, with a range of 98.60-99.10% identity. The highest average nucleotide identity (ANI), the highest digital DNA-DNA hybridization (DDH) values, and the average amino acid identity (AAI) with Neobacillus sp. PS3-40 reached 73.5%, 21.4%, and 75.54%, respectively. The major cellular fatty acids of strain Lsc_1132T included iso-C15:0, Summed Feature 3 (C16:1ω6c and/or C16:1ω7c), iso-C17:0, anteiso-C15:0, and iso-C17:1ω5c. The respiratory quinone of strains Lsc_1132T was MK-7. The G + C content of the genomic DNA was 40.9%. Based on the GTDB taxonomy and phenotypic data, strain Lsc_1132T could represent a novel species of a novel genus, proposed as Aliineobacillus hadale gen. nov. sp. nov. (type strain Lsc_1132T = MCCC 1K09620T). Metabolically, strain Lsc_1132T demonstrates a robust carbohydrate metabolism with many strain-specific sugar transporters. It also has a remarkable capacity for metabolizing amino acids and carboxylic acids. Genomic analysis reveals a streamlined genome in the organism, characterized by a significant loss of orthologous genes, including those involved in cytochrome c synthesis, aromatic compound degradation, and polyhydroxybutyrate (PHB) synthesis, which suggests its adaptation to low oxygen levels and oligotrophic conditions through alternative metabolic pathways. In addition, the reduced number of paralogous genes in strain Lsc_1132T, together with its high protein-coding gene density, may further contribute to streamlining its genome and enhancing its genomic efficiency. This research expands our knowledge of hadal microorganisms and their metabolic strategies for surviving in extreme deep-sea environments.

A new mesophilic member of the Chloroflexota phylum 'Ca. Сhloroploca septentrionalis' from the meromictic lake Bol'shie Khruslomeny separated from the White Sea.

A new filamentous phototrophic bacterium Khr17 was isolated as an enrichment culture from the brackish polar lake Bol'shie Khruslomeny. The organism was a halotolerant, strictly anaerobic phototroph possessing photosystem II. Sulfide was required for phototrophic growth. The cells of bacterium Khr17 formed nonmotile, wavy trichomes surrounded by a sheath. The cells contained chlorosomes, gas vesicles, and storage granules. The antenna pigments of bacterium Khr17 were bacteriochlorophyll c and β- and γ-carotenes. The genome of Khr17 bacterium carries all the genes responsible for CO2 fixation via the 3-hydroxypropionate pathway. The genes encoding the proteins of the nitrogenase complex were not found. The DNA G+C content was 59.9%. The 16S rRNA gene sequence of isolate Khr17 exhibited 99.4% similarity to related species. The average nucleotide identity and digital DNA-DNA hybridization values for the isolate showed 91.9% and 46.9% similarity, respectively, to other 'Ca. Chloroploca' species. Based on its phenotypic and phylogenetic characteristics, classification of Khr17 as member of a new species, 'Ca. Chloroploca septentrionalis' sp. nov., was proposed. Members of the genus 'Ca. Chloroploca' have previously not been found in Arctic areas and in the plankton of meromictic lakes.

Four novel nontuberculous mycobacteria species: Mycobacterium wendilense sp. nov., Mycobacterium burgundiense sp. nov., Mycobacterium kokjensenii sp. nov. and Mycobacterium holstebronense sp. nov. revived from a historical Danish strain collection.

Four novel nontuberculous mycobacteria were discovered from a historical strain collection at the International Reference Laboratory of Mycobacteriology at Statens Serum Institut in Copenhagen, Denmark. Phylogenetic analysis combining the 16S rrs, internal transcribed spacer and 23S rrl elements, as well as a single-copy core-gene (hsp65, rpoB+C, secA and tuf) analysis of these freeze-dried mycobacteria, clinically isolated from gastric lavage samples between 1948 and 1955, showed to be associated with type strains grouping within the Terra and Fortuitum-Vaccae clade. Phenotypic characteristics, biochemical properties and fatty acid and mycolic acid profiles supported the classification as novel strains. A genomic comparison to the closest related type strain was done by calculating average nucleotide identity and in silico DNA:DNA hybridization values, which showed 87.9% and 33.0% for Mu0050, 85.2% and 27.4% for Mu0053, 85.3% and 27.6% for Mu0083 and 93.3% and 50.1% for Mu0102, respectively. The names proposed for the new species are Mycobacterium wendilense sp. nov. (Mu0050T=ITM 501390T=CCUG 77525T), Mycobacterium burgundiense sp. nov. (Mu0053T=ITM 501391T=CCUG 77526T), Mycobacterium kokjensenii sp. nov. (Mu0083T=ITM 501392T=CCUG 77527T) and Mycobacterium holstebronense sp. nov. (Mu0102T=ITM 501393T=CCUG 77528T).

Analysis of the Genomes and Adaptive Traits of Skermanella cutis sp. nov., a Human Skin Isolate, and the Type Strains Skermanella rosea and Skermanella mucosa.

The genus Skermanella comprises important soil bacteria that are often associated with the crop rhizospheres, but its physiological traits remain poorly understood. This study characterizes Skermanella sp. TT6T, isolated from human skin, with a focus on its metabolic and environmental adaptations. Genome sequencing and phylogenomic analyses revealed that the strain TT6T is most closely related to S. rosea M1T, with average nucleotide identity and digital DNA-DNA hybridization values of 94.14% (±0.5%) and 64.7%, respectively. Comparative genomic analysis showed that the strains TT6T, S. rosea M1T and S. mucosa 8-14-6T share the Calvin cycle, and possess photosynthetic genes associated with the purple bacteria-type photosystem II. The strains TT6T and S. rosea M1T exhibited growth in a nitrogen-free medium under microaerobic conditions, which were generated in test tubes containing 0.1% soft agar. Under these conditions, with nitrate as a nitrogen source, S. rosea M1T formed gases, indicating denitrification. Strain TT6T also contains gene clusters involved in trehalose and carotenoid biosynthesis, along with salt-dependent colony morphology changes, highlighting its adaptive versatility. Genomic analyses further identified pathways related to hydrogenase and sulfur oxidation. Phenotypic and chemotaxonomic traits of strain TT6T were also compared with closely related type strains, confirming its genotypic and phenotypic distinctiveness. The new species, Skermanella cutis sp. nov., is proposed, with TT6T (=KCTC 82306T = JCM 34945T) as the type strain. This study underscores the agricultural and ecological significance of the genus Skermanella.

Streptococcus suivaginalis sp. nov., Streptococcus iners sp. nov. and Streptococcus iners subsp. hyiners subsp. nov. isolated from pigs.

Three novel strains within the genus Streptococcus (29887T, 29892T and 29896T) were isolated from healthy pigs during routine veterinary physical exams. All three strains were non-motile and non-spore-forming Gram-positive cocci. The complete genome of each strain was attained, and phylogenetic analyses were performed. Comparison of the genomes of 29887T, 29892T and 29896T to the genomes of other Streptococcus strains revealed digital DNA-DNA hybridization (dDDH) values between 21.2% and 53.9% and average nucleotide identity (ANI) values between 70.00% and 94.44%. Phylogenetic analyses suggested that each strain, 29896T (S. suivaginalis sp. nov.), 29887T (S. iners sp. nov.) and 29892T (S. iners subsp. hyiners subsp. nov.), may represent a novel species within the genus Streptococcus, while ANI analysis indicated that strains 29896T (S. suivaginalis sp. nov.) and 29887T (S. iners sp. nov.) represent novel species within the genus Streptococcus, and 29892T (S. iners subsp. hyiners subsp. nov.) represents a novel subspecies of 29887T (S. iners sp. nov.). Based upon the combined data presented in this study, two novel species, Streptococcus suivaginalis sp. nov. (type strain, 29896T=NRRL B-65677T=NCTC 14941T) and Streptococcus iners sp. nov. (type strain, 29887T=NRRL B-65675T=NCTC 14939T) are proposed, and one novel subspecies, Streptococcus iners subsp. hyiners subsp. nov. (type strain, 29892T=NRRL B-65676T=NCTC 14940T) is proposed.

Ascidiimonas meishanensis sp. nov. and Leptobacterium meishanense sp. nov., two bacteria isolated from marine sediment in the East China Sea.

Two Gram-stain-negative, curved-rod-shaped, non-motile and aerobic bacteria W6T and I13T were isolated from marine sediment samples collected from Meishan Island located in the East China Sea. Catalase and oxidase activities and hydrolysis of Tween 40, 60 and 80 were positive for both strains, while nitrate reduction, indole production, methyl red reaction and H2S production were negative. Phylogenetic analyses based on 16S rRNA and genome sequences revealed that strains W6T and I13T formed distinct phylogenetic lineages within the genera Ascidiimonas and Leptobacterium, respectively. Strain W6T showed the closest relatedness to Ascidiimonas aurantiaca N5DA8-2CT with 93.9% 16S rRNA gene sequence similarity, 70.7% average nucleotide identity (ANI), 71.0% average amino acid identity (AAI) and 16.4% digital DNA-DNA hybridization (dDDH) values, while strain I13T was most closely related to Leptobacterium flavescens YM3-301T with 92.1% 16S rRNA gene sequence similarity, 70.5% ANI, 72.1% AAI and 17.2% dDDH values. The two novel strains shared 92.0% 16S rRNA gene sequence similarity to each other and were identified as two distinct species based on 70.7% ANI, 70.4% AAI and 17.1% dDDH values calculated using whole-genome sequences. The genomes of strains W6T and I13T were 4.59 Mbp with a G+C content of 34.5 mol% and 2.38 Mbp with a G+C content of 36.2 mol%, respectively. The only respiratory quinone was menaquinone-6, the major polar lipid was phosphatidylethanolamine and the major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. Based on phenotypic, chemotaxonomic and genotypic data, strains W6T and I13T are considered to represent two novel species in the genera Ascidiimonas and Leptobacterium, respectively, in the family Flavobacteriaceae, for which the names Ascidiimonas meishanensis sp. nov. and Leptobacterium meishanense sp. nov. are proposed. The type strains are W6T (=KCTC 102201T=MCCC 1K08928T) and I13T (=KCTC 102202T=MCCC 1K08929T), respectively.

Using phenomic selection to predict hybrid values with NIR spectra measured on the parental lines: proof of concept on maize

Key messagePhenomic selection based on parental spectra can be used to predict GCA and SCA in a sparse factorial design.Prediction approaches such as genomic selection can be game changers in hybrid breeding. They allow predicting the genetic values of hybrids without the need for their physical production. This leads to significant reductions in breeding cycle length, and so to the increase in genetic progress. However, these methods are often underutilized in breeding programs due to the substantial cost involved in genotyping thousands of candidate parental lines annually. To address this limitation, we propose a cost-effective alternative based on phenomic selection, where genotyping of parental lines is replaced by NIR spectroscopy. Standard prediction models are then applied for genomic and phenomic selection, using similarity matrices derived from either genotyping data (genomic selection) or NIR spectral data (phenomic selection). Our hypothesis is that the chemical composition of parental tissues captured by NIRS reflects the genetic similarity between parental lines. We evaluated both strategies using a sparse factorial design, whose hybrids have been phenotyped in a multi-environment trial network, and with NIR spectra acquired on the parental lines on two independent environments. Both genomic and phenomic prediction approaches demonstrated moderate-to-high predictive abilities across various cross-validation scenarios. Our results also showcase the capability of phenomic selection to predict Mendelian sampling. This study serves as a proof of concept that low-cost high-throughput phenomics of parental lines can effectively be used to predict maize hybrids in independent trials. This paves the way for widespread adoption of prediction approaches at the very first stages of hybrid breeding, benefiting both major and orphan species.

Clostridium sediminicola sp. nov., a crude oil aggregation-forming anaerobic bacterium isolated from marine sediment.

A crude oil aggregation-forming, strictly anaerobic, Gram-stain-positive, spore-forming, rod-shaped, motile and mesophilic bacterium, named strain SH18-2T, was isolated from marine sediment near Sado Island in the Sea of Japan. The temperature, salinity and pH ranges of this strain for the growth were 15-40 °C (optimum 35 °C), 0.5-6.0% NaCl (w/v; optimum 2.0%) and pH 6.0-8.0 (optimum 7.5), respectively. A phylogenetic analysis of the 16S rRNA gene sequence showed that this strain belongs to the genus Clostridium. It was most closely related to Clostridium grantii A-1T (97.02% homology). The draft genome size was 5616089 bp, with a G+C content of 29.7 mol%. The digital DNA-DNA hybridization values determined using the Genome-to-Genome Distance Calculator and the average nucleotide identity between this strain and C. grantii A-1T were 20.30 and 78.24%, respectively. Whole-organism hydrolysates of strain SH18-2T contained meso-diaminopimelic acid; the major fatty acid was C16:0, and the polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, glycolipid and three unidentified polar lipids. From the results of genotypic, phenotypic and chemotaxonomic analyses, SH18-2T (=NBRC 116030T=DSM 115762T) is the type strain and represents a novel species of the genus Clostridium, and the name Clostridium sediminicola sp. nov. is proposed.

Pseudoalteromonas qingdaonensis sp. nov., isolated from the intestines of Ilyoplax deschampsi.

A Gram-stain-negative, aerobic, motile, catalase-positive, oxidase-positive, short rod-shaped marine bacterium, designated as YIC-827T, was isolated from Qingdao, Shandong Province, China. The results showed that cells of strain YIC-827T could grow optimally at 25-35 °C, pH 6.5-7.5 and 2-7% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that the strain YIC-827T was a member of the genus Pseudoalteromonas. The closest relative to this strain was Pseudoalteromonas ruthenica KMM 300T, with a similarity of 98.39%. The digital DNA-DNA hybridization value between the new isolate and phylogenetically related species is 19.6%. Strain YIC-827T could decompose sodium alginate, casein and esters (Tween 20, Tween 40, Tween 60 and Tween 80), but could not hydrolyse starch, cellulose and DNA. The fatty acid profile of a strain consists of a large number of C16:0, C18:1 ω7c and C16:1 ω7c/C16:1 ω6c. The G+C content of the DNA of this strain was determined to be 48.93%. Based on phenotypic characteristics, phylogenetic analysis and DNA-DNA correlation data, the strain YIC-827 T represents a novel species of the genus Pseudoalteromonas with the name Pseudoalteromonas qingdaonensis sp. nov. The type strain of P. qingdaonensis sp. is strain YIC-827T (=MCCC 1K08807T=CGMCC 1.62085T=KCTC 8212T).

Roseomonas cutis sp. nov., isolated from human epidermis.

Five pink-pigmented bacterial strains, isolated from human skin and classified within the genus Roseomonas, were examined. Among them, four were identified as Roseomonas mucosa, while strain OT10T was deemed to be a potential novel species. Strain OT10T exhibited characteristics, such as Gram-stain-negative, oxidase positive, motile, strictly aerobic and rod shaped. The cells had multiple flagella at one end, arranged in a lophotrichous pattern. The predominant cellular fatty acids in OT10T were C18:1 ω7c/C18:1 ω6c and C18:1 2OH; ubiquinone (Q)-10 was identified as the sole quinone. Major polar lipids included phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine and two aminolipids. The G+C content of the genome was determined to be 72.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarities revealed that strain OT10T is closely related to Roseomonas gilardii subsp. gilardii ATCC 49956T (97.7%), Roseomonas gilardii subsp. rosea ATCC BAA-691T (97.7%) and R. mucosa ATCC BAA-692T (97.5%). For the comparative genomic analyses, whole-genome sequencing was also conducted for strain OT10T. Considering the chemotaxonomic, genotypic and phenotypic features, as well as the low average nucleotide identity and digital DNA-DNA hybridization values compared to its closest phylogenomic neighbours, OT10T is proposed to be a novel species named Roseomonas cutis sp. nov., with OT10T designated as the type strain (=KCTC 92087T =JCM 34968T).

Flavobacterium magnesitis sp. nov. and Flavobacterium zubiriense sp. nov., two novel Flavobacterium species isolated from alkaline magnesite residues.

Three bacterial strains, designated FZUC8N2.13T, FBOR7N2.3T and FZUR7N2.5, were isolated from distinct magnesite residues in Spain. Phylogenetic and phylogenomic analysis places them within the genus Flavobacterium. Strains FBOR7N2.3T and FZUR7N2.5 share 100% of similarity in the 16S rRNA gene sequence, and both are most closely related to Flavobacterium cellulosilyticum AR-3-4T with which they share 97.5% of 16S rRNA gene similarity. Strain FZUC8N2.13T forms a distinct lineage most closely related to Flavobacterium lacustre IMCC36792T with 97.7% 16S rRNA gene similarity. The closest phylogenomic neighbours of these three strains are Flavobacterium flevense DSM 1076T, 'Flavobacterium undicola' BBQ-18T and Flavobacterium commune PK15T. The average nucleotide identity and digital DNA-DNA hybridization values between the three strains and closest members of the genus Flavobacterium are below the threshold values of 95% and 70%, respectively. Strains FZUC8N2.13T, FBOR7N2.3T and FZUR7N2.5 stain Gram-negative, are rod-shaped and form yellow colonies. Optimum growth occurs at 25 °C and pH 7. The genomic G+C contents are 33.4 mol% for strain FZUC8N2.13T and 33.2 mol% for strains FBOR7N2.3T and FZUR7N2.5. The major isoprenoid quinone is menaquinone 6. The major fatty acids are summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) (22.6-31.1%), iso-C15 : 0 (13.6-16.2 %) and anteiso-C15 : 0 (8.7-10.5%). The polar lipids consist of two aminolipids, two aminophospholipids and one glycolipid. The phylogenetic, phylogenomic, phenotypic and chemotaxonomic data indicate that FZUC8N2.13T, FBOR7N2.3T and FZUR7N2.5 are distinct from the described species of Flavobacterium and should be classified as novel species, for which we propose the names Flavobacterium zubiriense for strain FZUC8N2.13T (=UCCCB 179T=CECT 30977T) and Flavobacterium magnesitis for strains FBOR7N2.3T (=UCCCB 178T=CECT 30976T) and FZUR7N2.5 (=UCCCB 216=CECT 31036).

Pseudomonas fungipugnans sp. nov., a potently antifungal bacterium isolated from moss.

A novel strain, 681, was isolated from a moss sample taken from the Chrutzelried woods in Canton Zürich, Switzerland. The strain showed potent activity against several fungi and oomycetes. It was affiliated to the Pseudomonas genus by 16S rRNA gene sequence phylogeny. Genome sequencing showed a G+C content of 59.9 mol%. The highest average nucleotide identity was 86.63%, and the highest digital DNA-DNA hybridization value was 32.2% (with Pseudomonas nunensis ln5), considerably below the thresholds for species delineation. Multi-locus phylogeny using 81 concatenated sequences indicated that the strain represented a new species within the Pseudomonas mandelii subgroup. This study details its characterization as a new species. The 681 genome was screened in silico using antiSMASH to reveal candidate secondary metabolite clusters for the strong antifungal activity exhibited by 681. Of the 15 clusters identified, we disrupted the seven best and tested for activity against Fusarium solani. The pyrrolnitrin, rhizoxin, novel PKS-NRPS and acaterin gene clusters contributed significantly to the observed antifungal activity. Phenotypic analyses found that strain 681 cells were aerobic, Gram-negative, motile rods (mean length 2.60 µm and mean width of 0.67 µm) with one to three polar flagella. Optimal growth was at 30 °C, but growth also occurred at 8 °C. The pH range was 6-7, with some growth at pH 8. Robust growth occurred at 0-3% (w/v) NaCl and weak growth at 4% (w/v) NaCl, with the optimum at 1% (w/v) NaCl. Strain 681 was oxidase positive, hydrolysed arginine under anaerobic conditions, showed intense fluorescence on King's medium B and produced a hypersensitive response in tobacco leaves. Following our investigations, we propose the designation Pseudomonas fungipugnans sp. nov. for this new species. The type strain, 681, is available from the DSMZ and LMG/BCCM culture collections under the designations DSM 115721 and LMG 33039, respectively.

Description of Massilia orientalis sp. nov., Isolated from Rhizosphere Soil of Ageratina adenophora.

A novel bacteria strain, designated YIM B02787T, was isolated from rhizosphere soil of Ageratina adenophora, in Yunnan, southwest China. The strain was aerobic, Gram-stain-negative, rod-shaped and motile with one polar flagellum. Growth occurred at 4-45°C (optimum, 20-30°C) and pH 6.0-10.0 (optimum, 7.0-8.0), and in presence of 0-1% (w/v) NaCl. Phylogenetic analyses based on both 16S rRNA gene and genome sequences data revealed that strain YIM B02787T belongs to the genus Massilia, being closely related to Massilia phosphatilytica KCTC 52513T (98.93% similarity), M. putida KCTC 42761T (98.86%), and M. kyonggiensis JCM 19189T (98.78%). The DNA G+C content was 65.9%. The digital DNA-DNA hybridization and average nucleotide identity values between the isolate strain and aforementioned closely neighbors were low, at 35.8-48.9 and 88.5-92.5%, respectively. Strain YIM B02787T contained Q-8 as the ubiquinone and major fatty acids were summed feature 3 (C16:1ω7c and/or C16:1ω6c, 45.5%) and C16:0 (27.5%). The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, two unidentified phospholipids, two unidentified aminophospholipids, and one unidentified polar lipid. On the basis of its phylogenetic, phenotypic and chemotaxonomic characteristics, strain YIM B02787Trepresents a novel species of the genus Massilia, for which the name Massilia orientalis sp. nov. is proposed. The type strain is YIM B02787T (= NBRC 116628T = CGMCC 1.61539T).

Sphingomonas longa sp. nov., Sphingomonas mollis sp. nov. and Sphingomonas aurea sp. nov.: three novel Sphingomonas species isolated from soil.

Three Gram-negative, aerobic and non-motile bacterial strains, BT552T, BT553T and KR1UV-12T, were isolated from soil samples in Gwangju-si and Gangneung-si, the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequence showed that strains BT552T, BT553T and KR1UV-12T clustered to a distinct clade within the family Sphingomonadaceae (order Sphingomonadales, class Alphaproteobacteria). The strains exhibited the highest genetic similarity with representatives of the genus Sphingomonas; moreover, strains BT552T and BT553T tightly clustered with Sphingomonas melonis DAPP-PG 224T (98.2 and 98.1 %) and Sphingomonas aquatilis JSS-7T (98.1 and 98.0 %), while strain KR1UV-12T clustered with S. melonis DAPP-PG 224T (97.9%) and Sphingomonas rubra BH3T (97.8%), respectively. The major cellular fatty acids of all three strains were summed feature 8 (C18:1 ω7c/C18:1 ω6c), comprising 44.7, 46.4 and 48.5%. Additionally, their respiratory quinone is Q-10, and polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phospholipids, sphingolipid and phosphatidylcholine. They all grow well at an optimum temperature of 25 °C, at pH 7. The draft genomes of strains BT552T, BT553T and KR1UV-12T measures 4 035 561 bp, 3 941 714 bp and 3 418 792 bp, respectively, comprising 3 804 3648 and 3236 coding sequences and 50, 48 and 45 RNA genes. The average nucleotide identity analysis and digital DNA-DNA hybridization values between BT552T, BT553T and KR1UV-12T and closely related Sphingomonas species range from 72.7 to 80.2% and 19.4 to 24.3%, respectively. Based on phenotypic, genotypic and chemotaxonomic data, these three strains BT552T, BT553T and KR1UV-12T represent three novel bacterial species within the genus Sphingomonas for which the names Sphingomonas longa sp. nov. (type strain BT552T= KCTC 82094T =NBRC 114993T), Sphingomonas mollis sp. nov. (type strain BT553T =KCTC 82095T =NBRC 114994T) and Sphingomonas aurea sp. nov. (type strain KR1UV-12T = KCTC 92959T = TBRC 18506T) are proposed.