Description of Hymenobacter arizonensis sp. nov. from the southwestern arid lands of the United States of America

Hymenobacter canadensis sp. nov., isolated from freshwater of the pond in Cambridge Bay, Canada

A Gram-stain-negative, aerobic, reddish-coloured, rod-shaped and non-motile strain PAMC 29467^T, was isolated from freshwater of the pond in Cambridge Bay, Canada. Strain PAMC 29467^T was closely related to Hymenobacter yonginensis (98.1 % 16S rRNA gene similarity). Genomic relatedness analyses showed that strain PAMC 29467^T is distinguishable from H. yonginensis based on average nucleotide identity (91.3 %) and digital DNA-DNA hybridization values (39.3 %). The major fatty acids (>10 %) of strain PAMC 29467^T were summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), C_15 : 0 iso, C_16 : 1  ω5c and summed feature 4 (C_17 : 1 iso l and/or anteiso B). The major respiratory quinone was menaquinone-7. The genomic DNA G+C content was 61.5 mol%. Strain PAMC 29467^T was separated from the type species in the genus Hymenobacter by its distinct phylogenetic position and some physiological characteristics. As a result, a novel species is proposed, with the name Hymenobacter canadensis sp. nov. (type strain, PAMC 29467^T=KCTC 92787^T=JCM 35843^T).

Hymenobacter terricola sp. nov., isolated from Antarctic soil

Strain 3F2T was isolated from a soil sample obtained from the surface of Deception Island, Antarctica. The isolate was a Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, and its colonies were red to pink in colour. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 3F2T belonged to the genus Hymenobacter , family Hymenobacteraceae and was most closely related to Hymenobacter sedentarius DG5BT (97.0% sequence similarity), Hymenobacter soli PB17T (96.9%), Hymenobacter terrae DG7AT (96.8%) and Hymenobacter rufus S1-2-2-6T (96.5%). Growth occurred at 4–20 °C (optimum, 10 °C), up to 1.0 % (w/v) NaCl (optimum, 0%) and pH 6.0–8.0 (optimum, pH 7.0). The chemotaxonomic characteristics of strain 3F2T, which had MK-7 as its predominant menaquinone and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), iso-C15:0, anteiso-C15:0 and C16:1 ω5c as its major fatty acids, were consistent with classification in the genus Hymenobacter . The polar lipid profile of strain 3F2T comprised phosphatidylethanolamine, two unidentified aminolipids, two unidentified aminophospholipids and three unidentified polar lipids. The genome of strain 3F2T was 6.56 Mbp with a G+C content of 61.5 mol%. Average nucleotide identity (ANI) values between 3F2T and the other species of the genus Hymenobacter were found to be low (ANIm <87.0%, ANIb <82.0% and OrthoANIu <83.0%). Furthermore, digital DNA–DNA hybridization and average amino acid identity values between strain 3F2T and the closely related species ranged from 20.0 to 26.3% and from 64.0 to 81.1 %, respectively. Based on the results of our phylogenetic, phenotypic, genotypic and chemotaxonomic analyses, it is concluded that strain 3F2T represents a novel species within the genus Hymenobacter , for which the name Hymenobacter terricola sp. nov. is proposed. The type strain is 3F2T (=KCTC 72468T=CGMCC 1.13716T).

Hymenobacter taeanensis sp. nov., radiation resistant bacterium isolated from coastal sand dune

An aerobic, Gram-stain-negative, non-motile, non-spore-forming, rod-shaped, and light pink-colored bacterial strain, designated TS19^T, was isolated from a sand sample obtained from a coastal sand dune after exposure to 3 kGy of gamma radiation. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the isolate was a member of the genus Hymenobacter and was most closely related to H. wooponensis WM78^T (98.3% similarity). Strain TS19^T and H. wooponensis showed resistance to gamma radiation with D₁₀ values (i.e., the dose required to reduce the bacterial population by tenfold) of 7.3 kGy and 3.5 kGy, respectively. The genome of strain TS19^T consists of one contig with 4,879,662 bp and has a G + C content of 56.2%. The genome contains 3,955 protein coding sequences, 44 tRNAs, and 12 rRNAs. The predominant fatty acids of strain TS19^T were iso-C_15:0, summed feature 4 (iso-C_17:1 I and/or anteiso-C_17:1 B), summed feature 3 (C_16:1 ω6c and/or C_16:1 ω7c), and C_16:1 ω5c. The major polar lipids were phosphatidylethanolamine, and one unidentified aminophospholipid. The main respiratory quinone was menaquinone-7. Based on the phylogenetic, physiological, and chemotaxonomic characteristics, strain TS19^T represents a novel species, for which the name Hymenobacter taeanensis sp. nov. is proposed. The type strain is TS19^T (= KCTC 72897^T = JCM 34023^T).

Extremophilic microbial communities on photovoltaic panel surfaces: a two-year study

Solar panel surfaces can be colonized by microorganisms adapted to desiccation, temperature fluctuations and solar radiation. Although the taxonomic and functional composition of these communities has been studied, the microbial colonization process remains unclear. In the present work, we have monitored this microbial colonization process during 24 months by performing weekly measurements of the photovoltaic efficiency, carrying out 16S rRNA gene high-throughput sequencing, and studying the effect of antimicrobial compounds on the composition of the microbial biocenosis. This is the first time a long-term study of the colonization process of solar panels has been performed, and our results reveal that species richness and biodiversity exhibit seasonal fluctuations and that there is a trend towards an increase or decrease of specialist (solar panel-adapted) and generalist taxa, respectively. On the former, extremophilic bacterial genera Deinococcus, Hymenobacter and Roseomonas and fungal Neocatenulostroma, Symmetrospora and Sporobolomyces tended to dominate the biocenosis; whereas Lactobacillus sp or Stemphyllium exhibited a decreasing trend. This profile was deeply altered by washing the panels with chemical agents (Virkon), but this did not lead to an increase of the solar panels efficiency. Our results show that solar panels are extreme environments that force the selection of a particular microbial community.

Validating biochemical features at the genome level in the Antarctic bacterium Hymenobacter sp. strain UV11

We present experimental data that complement and validate some biochemical features at the genome level in the UVC-resistant Antarctic bacterium Hymenobacter sp. UV11 strain. The genome was sequenced, assembled and annotated. It has 6 096 246 bp, a GC content of 60.6% and 5155 predicted genes. The secretome analysis, by combining in silico predictions with shotgun proteomics data, showed that UV11 strain produces extracellular proteases and carbohydrases with potential biotechnological uses. We observed the formation of outer membrane vesicles, mesosomes and carbon-storage compounds by using transmission electron microscopy. The in silico analysis of the genome revealed the presence of genes involved in the metabolism of glycogen-like molecules and starch. By HPLC-UV-Vis analysis and 1H-NMR spectra, we verified that strain UV11 produces xanthophyll-like carotenoids such as 2'-hydroxyflexixanthin, and the in silico analysis showed that this bacterium has genes involved in the biosynthesis of cathaxanthin, zeaxanthin and astaxanthin. We also found genes involved in the repair of UV-damaged DNA such as a photolyase, the nucleotide excision repair system and the production of ATP-dependent proteases that are important cellular components involved in the endurance to physiological stresses. This information will help us to better understand the ecological role played by Hymenobacter strains in the extreme Antarctic environment.

Hymenobacter lutimineralis sp. nov., belonging to the family Hymenobacteraceae, isolated from zeolite

A red-pigmented bacterial strain, designated KIGAM108^T, within the family Hymenobacteraceae was isolated from zeolite in the Gampo-41 mine of the Gyeongju, Republic of Korea. This strain was a Gram-negative, strictly aerobic, non-spore forming, rod-shaped bacterium. Phylogenetic analysis of the 16S rRNA gene sequence of strain KIGAM108^T found that it was related to the genus Hymenobacter, with similarities of 96.6, 96.4, 95.5, and 95.0% to H. fastidiosus VUG-A124^T, H. algoricola VUG-A23a^T, H. crusticola MIMBbqt21^T, and H. daecheongensis DSM 21074^T, respectively. Strain KIGAM108^T grew in the presence of 0-0.5% (w/v) NaCl at 4-37 °C and pH 6.0-10.0. This isolate contained MK-7 as a respiratory quinone. The polar lipids of strain KIGAM108^T were identified as phosphatidylethanolamine, two unidentified aminophospholipids, one unidentified phospholipid and five unidentified lipids. The major fatty acids profile showed summed feature 3 (C_16:1ω6c and/or C_16:1ω7c) (22.3%), anteiso-C_15:0 (17.1%), C_16:1ω5c (13.3%), and iso-C_15:0 (11.0%). The genomic DNA G + C content was 60.0 mol%. Based on the polyphasic taxonomic data, strain KIGAM108^T is considered to represent a novel species of the genus Hymenobacter, for which the name Hymenobacter lutimineralis sp. nov. is proposed. The type strain is KIGAM108^T (=KCTC 72263^T =JCM 33444^T).

Hymenobacter sediminis sp. nov., isolated from lake sediment

A Gram-stain-negative, facultatively aerobic, rod-shaped, motile by gliding and pink-pigmented bacterial strain, designated ELS1360^T, was isolated from a lake sediment sample collected in Inner Mongolia, PR China. Strain ELS1360^T grew optimally at 33 °C, at pH 6.5-7.0 and without NaCl. Strain ELS1360^T exhibited 97.3, 97.1 and 96.9 % 16S rRNA gene sequence similarities to Hymenobacter aquatilis HMF3095^T, Hymenobacter luteus JCM 30328^T and Hymenobacter latericoloratus JCM 30327^T, respectively, and 90.4-96.9 % to other members of the genus Hymenobacter. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain ELS1360^T belonged to the genus Hymenobacter and clustered with H. luteus JCM 30328^T and H. latericoloratus JCM 30327^T. The predominant cellular fatty acids were iso-C_15:0, summed feature 3 and C_16:1ω5c. Strain ELS1360^T contained MK-7 as the sole menaquinone. The major polar lipids contained phosphatidylethanolamine and two unidentified lipids. The genomic DNA G+C content of strain ELS1360^T was 57.1 mol%. Based on the results of our phylogenetic, phenotypic, genotypic and chemotaxonomic analyses, it is concluded that strain ELS1360^T represents a novel species within the genus Hymenobacter, for which the name Hymenobacter sediminis sp. nov. is proposed. The type strain is ELS1360^T (=KCTC 62449^T=MCCC 1H00319^T).

Biological Ice-Nucleating Particles Deposited Year-Round in Subtropical Precipitation

Airborne bacteria that nucleate ice at relatively warm temperatures (>-10°C) can interact with cloud water droplets, affecting the formation of ice in clouds and the residency time of the cells in the atmosphere. We sampled 65 precipitation events in southeastern Louisiana over 2 years to examine the effect of season, meteorological conditions, storm type, and ecoregion source on the concentration and type of ice-nucleating particles (INPs) deposited. INPs sensitive to heat treatment were inferred to be biological in origin, and the highest concentrations of biological INPs (∼16,000 INPs liter^-1 active at ≥-10°C) were observed in snow and sleet samples from wintertime nimbostratus clouds with cloud top temperatures as warm as -7°C. Statistical analysis revealed three temperature classes of biological INPs (INPs active from -5 to -10°C, -11 to -12°C, and -13 to -14°C) and one temperature class of INPs that were sensitive to lysozyme (i.e., bacterial INPs, active from -5 to -10°C). Significant correlations between the INP data and abundances of taxa in the Bacteroidetes, Firmicutes, and unclassified bacterial divisions implied that certain members of these phyla may possess the ice nucleation phenotype. The interrelation between the INP classes and fluorescent dissolved organic matter, major ion concentrations (Na⁺, Cl^-, SO₄ ^2-, and NO₃ ^-), and backward air mass trajectories indicated that the highest concentrations of INPs were sourced from high-latitude North American and Asian continental environments, whereas the lowest values were observed when air was sourced from marine ecoregions. The intra- and extracontinental regions identified as sources of biological INPs in precipitation deposited in the southeastern United States suggests that these bioaerosols can disperse and affect meteorological conditions thousands of kilometers from their terrestrial points of origin.IMPORTANCE The particles most effective at inducing the freezing of water in the atmosphere are microbiological in origin; however, information on the species harboring this phenotype, their environmental distribution, and ecological sources are very limited. Analysis of precipitation collected over 2 years in Louisiana showed that INPs active at the warmest temperatures were sourced from terrestrial ecosystems and displayed behaviors that implicated specific bacterial taxa as the source of the ice nucleation activity. The abundance of biological INPs was highest in precipitation from winter storms and implied that their in-cloud concentrations were sufficient to affect the formation of ice and precipitation in nimbostratus clouds.

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

Hymenobacter persicinus sp. nov., a novel member of the family Hymenobacteraceae

A bacterial strain, 1-3-3-3^T, was isolated from a soil sample collected in Jeollabuk-do province, South Korea. Cells were observed to be Gram-stain negative, short rod-shaped and colonies to be red-pink in colour. Analysis of 16S rRNA gene sequences identified this strain as a member of the genus Hymenobacter in the family Hymenobacteraceae, with high levels of 16S rRNA sequence similarity with Hymenobacter algoricola VUG-A23a^T (98.0%), Hymenobacter knuensis 16F7C-2 (97.9%), Hymenobacter fastidiosus VUG-A124^T (97.1%), Hymenobacter elongatus VUG-A112^T (97.0%), Hymenobacter chitinivorans Txc1^T (97.0%) and Hymenobacter aquaticus 16F3P^T (96.7%). Growth of strain 1-3-3-3^T was observed at 10-30 °C, pH 6-8 and in the presence of 0-1.0% NaCl. The genomic G + C content was determined to be 61.6 mol %. The predominant respiratory quinone of the isolate was found to be MK-7; the major fatty acids were identified as iso-C_15:0 (19.9%), summed feature 3 (C_16:1ω7c/C_16:1ω6c, 19.7%), summed feature 4 (iso-C_17:1 I/anteiso-C_17:1 B, 17.8%), C_16:1ω5c (12.5%) and anteiso-C_15:0 (11.2%), and the major polar lipid was found to be phosphatidylethanolamine. The phenotypic and chemotaxonomic data support the affiliation of strain 1-3-3-3^T with the genus Hymenobacter. However, the DNA-DNA relatedness between the isolate and its closest phylogenetic neighbours was lower than 34%. The DNA-DNA hybridization result and the differentiating phenotypic properties clearly indicate that strain 1-3-3-3^T represents a novel species in the genus Hymenobacter, for which the name Hymenobacter persicinus sp. nov. is proposed. The type strain is 1-3-3-3^T (= KCTC 52742^T = JCM 32191^T).

Hymenobacter crusticola sp. nov., isolated from biological soil crust

A Gram-stain-negative, aerobic, light-pink, short rod-shaped, non-spore-forming bacterial strain was isolated from biological soil crust sampled in the Hopq Desert, Inner Mongolia, China, designated MIMBbqt21^T. The G+C content of the genomic DNA was 55.1 mol%. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain MIMBbqt21^T belonged to the genus Hymenobacter and had the highest sequence similarity to Hymenobacter cavernaeK1E01-27^T (94.35 %). Cell growth could be observed at 4-29 °C (optimum, 24 °C), pH of 6.0-8.6 (optimum, 6.0) and in the presence of 1 % (w/v) NaCl (optimum, 0 %). The major fatty acids of strain MIMBbqt21^T were iso-C15 : 0, C16 : 1ω5c and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). The main polar lipids were phosphatidylethanolamine, five unidentified aminophospholipids, an unidentified glycolipid and four unidentified polar lipids. The sole respiratory quinone was menaquinone MK-7. Based on the results of the phylogenetic, chemotaxonomic and phenotypic studies, strain MIMBbqt21^T could be distinguished from all known Hymenobacter species and represents a novel species, for which the name Hymenobactercrusticola sp. nov. is proposed. The type strain is MIMBbqt21^T (=MCCC 1K01312^T=KCTC 42804^T).

Hymenobacter pomorum sp. nov., Isolated from Apple Orchard Soil

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, designated 9-2-1-1^T, was isolated from apple orchard soil in Daegu, Republic of Korea. Comparative 16S rRNA gene sequence analysis showed that the isolate belongs to the family Cytophagaceae, Bacteroidetes and it is most closely related to Hymenobacter metalli A2-91^T (97.8% similarity) and Hymenobacter marinus KJ035^T (96.6%). Growth of strain 9-2-1-1^T was observed at 4-30 °C, pH 6-8, and in the presence of 0-1.0% NaCl. The G+C content of the genomic DNA was 62.0 mol%. The predominant respiratory quinone of the isolate was MK-7; the major fatty acids were C_15:0 iso (29.3%), C_16:1ω5c (15.4%), C_15:0 anteiso (12.5%), summed feature 3 (C_16:1ω7c/C_16:1ω6c; 12.3%), and C_16:0 (10.6%); and the major polar lipid was phosphatidylethanolamine. The phenotypic and chemotaxonomic data supported the affiliation of strain 9-2-1-1^T with the genus Hymenobacter. However, the DNA-DNA relatedness between the isolate and H. metalli and H. marinus were 31.3% and 24.7%, respectively. The DNA-DNA hybridization result and the differentiating phenotypic properties clearly indicate that strain 9-2-1-1^T is the representative of a novel species in the genus Hymenobacter, for which the name Hymenobacter pomorum sp. nov. is proposed. The type strain is 9-2-1-1^T (=KCTC 52740^T = JCM 32193^T).

Hymenobacter rufus sp. nov., a bacterium isolated from soil

A bacterial strain, S1-2-2-6^T, was isolated from a soil sample collected in Jeollabuk-do province, Republic of Korea. Cells of this strain were observed to be Gram-stain-negative, short and rod-shaped, and colonies were red to pink in colour. Analysis of 16S rRNA gene sequences identified this strain as representing a member of the genus Hymenobacter in the family Cytophagaceae, with the highest levels of sequence similarity being observed in relation to Hymenobacter terrae DG7A^T (98.2 %), Hymenobacter rubidus DG7B^T (97.9 %), Hymenobacter soli PB17^T (97.7 %), and Hymenobacter daeguensis 16F3Y-2^T (97.3 %). Growth of S1-2-2-6^T was observed at 4-30 °C, pH 6-8 and in the presence of 0-0.5 % NaCl. The predominant respiratory quinone of this strain was menaquinone-7, the major fatty acids were C15 : 0 iso, C15 : 0 anteiso, and Summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), and the major polar lipid was phosphatidylethanolamine. The genomic DNA G+C content of S1-2-2-6^T was 60.7 mol%. DNA-DNA hybridization experiments with H. terrae, H. rubidus, H. soli and H. daeguensisresulted in relatedness values of 35.9 and 38.4 %, 34.2 and 30.4 %, 28.3 and 33.1 %, and 23.5 and 27.9 %, respectively. These DNA-DNA hybridization results, in addition to some differentiating phenotypic properties, clearly indicate that S1-2-2-6^T is a representative of a novel species of the genus Hymenobacter, for which the name Hymenobacter rufus sp. nov. is proposed. The type strain is S1-2-2-6^T (=KCTC 52736^T=JCM 32196^T).

Hymenobacter jeollabukensis sp. nov., isolated from soil

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterial strain, designated 1-3-3-8^T, was isolated from soil and characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain 1-3-3-8^T belongs to the family Cytophagaceae of phylum Bacteroidetes and is most closely related to Hymenobacter paludis KBP-30^T (96.8% similarity), Hymenobacter ocellatus Myx2105^T (96.8%), Hymenobacter coalescens WW84^T (95.6%), and Hymenobacter deserti ZLB-3^T (95.4%). The G + C content of the genomic DNA of strain 1-3-3-8^T was 63.6 mol%. The isolate contained C_15:0 iso (28.4%), summed feature 4 (C_17:1 anteiso B/C_17:1 iso I; 18.9%), and C_15:0 anteiso (17.6%) as major fatty acids, MK-7 as the predominant respiratory quinone, and sym-homospermidine as the predominant polyamine. The major polar lipids were phosphatidylethanolamine and an unidentified lipid. The phenotypic and chemotaxonomic data supported the affiliation of strain 1-3-3-8^T with the genus Hymenobacter. The DNA-DNA relatedness between strain 1-3-3-8^T and H. paludis KCTC 32237^T and H. ocellatus DSM 11117^T were 24.5 and 27.4% respectively, clearly showing that the isolate is not related to them at the species level. Overall, the novel strain could be differentiated from its phylogenetic neighbors on the basis of several phenotypic, genotypic, and chemotaxonomic features. Therefore, strain 1-3-3-8^T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter jeollabukensis sp. nov. has been proposed. The type strain is 1-3-3-8^T (= KCTC 52741^T = JCM 32192^T).

Hymenobacter segetis sp. nov., isolated from soil

A polyphasic taxonomic study was performed on a novel strain designated as S7-3-11^T, which was isolated from soil of the Gyeongsangnam-do province in Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain S7-3-11^T belongs to the genus Hymenobacter and is most closely related to Hymenobacter ruber PB156^T (97.9%), Hymenobacter daeguensis 16F3Y-2^T (97.8%), Hymenobacter glaciei VUG-A130^T (97.7%), Hymenobacter soli PB17^T (97.5%), Hymenobacter terrae DG7A^T (97.5%), and Hymenobacter antarcticus VUG-A42aa^T (97.3%). However, DNA-DNA hybridization results showed less than 50% relatedness with respect to the type strains of the six most closely related species. The DNA G + C content of strain S7-3-11^T was 60.2 mol%. MK-7 was identified as the predominant respiratory quinone, and summed feature 3 (C_16:1 ω7c/C_16:1 ω6c; 21.5%), C_15:0 iso (16.8%), C_15:0 anteiso (16.2%), and C_15:1 iso G (10.8%) were the major fatty acids. Phosphatidylethanolamine, an unidentified aminolipid, and an unidentified aminophospholipid were detected as major polar lipids. On the basis of the polyphasic evidence presented, strain S7-3-11^T is considered to represent a novel species of the genus Hymenobacter, for which the name Hymenobacter segetis sp. nov. is proposed. The type strain is S7-3-11^T (= KCTC 52732^T = JCM 32197^T).

Hymenobacter pedocola sp. nov., a novel bacterium isolated from soil

Strain S12-2-1^T was isolated from a soil sample collected in the Gyeongsangnam-do province of the Republic of Korea. The isolate is a Gram-stain-negative, aerobic, short, rod-shaped bacterium, and its colonies are red to pink in colour. Analysis of the 16S rRNA gene identified strain S12-2-1^T as a member of the genus Hymenobacter in the family Cytophagaceae, with high levels of 16S rRNA gene sequence similarity to Hymenobacter arizonensis OR362-8^T (97.7 %), Hymenobacter sedentarius DG5B^T (97.4 %) and Hymenobacter humi DG31A^T (97.2 %). The isolate was positive for catalase and oxidase, but negative for acid production from glucose. The growth of strain S12-2-1^T was supported at 4-30 °C, pH 7-10 and in the presence of 0-0.5 % NaCl. Strain S12-2-1^T contained menaquinone-7 as the predominant respiratory quinone, sym-homospermidine as the major polyamine and iso-C15 : 0, anteiso-C15 : 0 and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) as the major fatty acids. Phosphatidylethanolamine was the major polar lipid. The genomic DNA G+C content was 58.7 mol%. Phenotypic and chemotaxonomic data supported the assignment of the isolate to the genus Hymenobacter. However, strain S12-2-1^T exhibited a relatively low level of DNA-DNA relatedness with H. humi (31.7 %), H. arizonensis (24.4 %) and H. sedentarius (21.3 %). Based on its phenotypic and genotypic properties, along with its phylogenetic distinctiveness, strain S12-2-1^T should be considered a novel species in the genus Hymenobacter, for which the name Hymenobacter pedocola sp. nov. is proposed. The type strain is S12-2-1^T (=KCTC 52730^T=JCM 32198^T).

Hymenobacter daeguensis sp. nov. isolated from river water

A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped, aerobic bacterial strain, designated 16F3Y-2^T, was isolated from the Han River, South Korea, and was characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain 16F3Y-2^T belonged to the family Cytophagaceae in the phylum Bacteroidetes and was most closely related to 'Hymenobacter terrae' DG7A (98.01%), H. soli PB17^T (97.26%), H. glaciei VUG-A130^T (96.78%), H. antarcticus VUG-A42aa^T (96.72%), H. ruber PB156^T (96.61%), and H. saemangeumensis GSR0100^T (95.77%). The G+C content of the genomic DNA of strain 16F3Y-2^T was 62.9 mol%. The isolate contained MK-7 as the predominant respiratory quinone, and summed feature 3 (C_16:1 ω7c/C_16:1 ω6c; 35.5%), C_15:0 iso (16.9%), C_16:1 ω5c (10.9%), and C_15:0 anteiso (9.9%) as major fatty acids. The major polar lipid was phosphatidylethanolamine. Phenotypic and chemotaxonomic data supported the affiliation of strain 16F3Y-2^T with the genus Hymenobacter. However, strain 16F3Y-2^T exhibited relatively low levels of DNA-DNA relatedness with 'H. terrae' KCTC 32554 (44.1%) and H. soli KCTC 12607^T (24.3%), clearly indicating that the isolate constitutes a new genospecies. Strain 16F3Y-2^T could be differentiated from its phylogenetic neighbors on the basis of several phenotypic, genotypic, and chemotaxonomic features. Therefore, strain 16F3Y-2^T represents a novel species in the genus Hymenobacter, for which the name Hymenobacter daeguensis sp. nov. is proposed. The type strain is 16F3Y-2^T (=KCTC 52537^T =JCM 31654^T).

Description of Deinococcus oregonensis sp. nov., from biological soil crusts in the Southwestern arid lands of the United States of America

Biological soil crusts are distinct habitats, harbor unique prokaryotic diversity and gave an impetus to isolate novel species. In the present study, a pink-pigmented bacterium, (OR316-6^T), was isolated from biological soil crusts using oligotrophic BG11-PGY medium. Strain OR316-6^T was Gram-positive, short rods, non-motile and non-spore forming. Cells were positive for catalase, oxidase and β-galactosidase and negative for most of the enzymatic activities. The major fatty acids present were C_16:0, C_17:0, and C_16:1ω7c and contained MK-8 and MK-10 as the predominant menaquinones. The cell wall peptidoglycan was of A3β variant with L-ornithine as the diamino acid. Based on the above characteristics, strain OR316-6^T was assigned to the genus Deinococcus. The phylogenetic analysis indicated that strain OR316-6^T was closely related to D. aquatilis DSM 23025^T with a 16S rRNA gene similarity of 99.3 % and clustered with a bootstrap value of 100 %. DNA-DNA similarity between strain OR316-6^T and D. aquatilis DSM 23025^T was 37.0 % indicating that strain OR316-6^T was a novel species. Further, DNA fingerprinting of stains OR316-6^T and D. aquatilis DSM 23035^T demonstrated that both strains were related to each other with a similarity coefficient of only 0.32 and supported the species status to strain OR316-6^T. In addition, phenotypic characteristics distinguished strain OR316-6^T from D. aquatilis DSM 23025^T. Based on the cumulative differences, strain OR316-16^T exhibited with its closely related species, it was identified as a novel species and proposed the name Deinococcus oregonensis sp. nov. The type strain is D. oregonensis sp. nov. (OR316-6^T = JCM 13503^T = DSM 17762^T).

Hymenobacter terrenus sp. nov., isolated from biological soil crusts

A Gram-stain-negative, non-spore-forming, short rod-shaped, non-motile, light-pink bacterial strain, MIMtkLc17T, was isolated from biological soil crusts collected in Liangcheng, Inner Mongolia. Growth of strain MIMtkLc17T was observed at 2–35 °C and in the presence of 1% (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences showed that sequence similarities between strain MIMtkLc17T and the type strains of species of the genus Hymenobacter ranged from 89.93% to 96.49%. Strain MIMtkLc17T can secrete mass polysaccharide. The major fatty acids of strain MIMtkLc17T were iso-C15 : 0, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), C16 : 1ω5c and summed feature 4 (iso-C17 : 1 I/anteiso-C17 : 1 B). The sole respiratory quinone was menaquinone MK-7. The G+C content of the chromosomal DNA was 57.8 mol%. The results of phylogenetic, chemotaxonomic and phenotypic characterization indicated that strain MIMtkLc17T can be distinguished from all known species of the genus Hymenobacter and represents a novel species of this genus, for which the name Hymenobacter terrenus sp. nov. is proposed. The type strain is MIMtkLc17T ( = MCCC 1K00507T = KCTC 42636T).

Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust

Biological Soil Crusts (BSCs) are organosedimentary assemblages comprised of microbes and minerals in topsoil of terrestrial environments. BSCs strongly impact soil quality in dryland ecosystems (e.g., soil structure and nutrient yields) due to pioneer species such as Microcoleus vaginatus; phototrophs that produce filaments that bind the soil together, and support an array of heterotrophic microorganisms. These microorganisms in turn contribute to soil stability and biogeochemistry of BSCs. Non-cyanobacterial populations of BSCs are less well known than cyanobacterial populations. Therefore, we attempted to isolate a broad range of numerically significant and phylogenetically representative BSC aerobic heterotrophs. Combining simple pre-treatments (hydration of BSCs under dark and light) and isolation strategies (media with varying nutrient availability and protection from oxidative stress) we recovered 402 bacterial and one fungal isolate in axenic culture, which comprised 116 phylotypes (at 97% 16S rRNA gene sequence homology), 115 bacterial and one fungal. Each medium enriched a mostly distinct subset of phylotypes, and cultivated phylotypes varied due to the BSC pre-treatment. The fraction of the total phylotype diversity isolated, weighted by relative abundance in the community, was determined by the overlap between isolate sequences and OTUs reconstructed from metagenome or metatranscriptome reads. Together, more than 8% of relative abundance of OTUs in the metagenome was represented by our isolates, a cultivation efficiency much larger than typically expected from most soils. We conclude that simple cultivation procedures combined with specific pre-treatment of samples afford a significant reduction in the culturability gap, enabling physiological and metabolic assays that rely on ecologically relevant axenic cultures.

Hymenobacter humi sp. nov., a bacterium isolated from soil

A red-pink coloured, Gram-negative, rod-shaped bacterium designated as strain DG31A(T) was isolated from soil collected in Seoul, South Korea. The isolate was found to grow optimally at 25 °C on R2A agar. The highest degrees of 16S rRNA gene sequence similarities of the strain were found with Hymenobacter arizonensis JCM 13504(T) (98.0 %), Hymenobacter glaciei VUG-A130(T) (96.1 %), Hymenobacter soli PB17(T) (95.2 %), Hymenobacter antarcticus VUG-A42aa(T) (94.7 %) and Hymenobacter chitinivorans Txc1(T) (92.8 %). The DNA G+C content of the novel strain, DG31A(T), was determined to be 60.8 mol%. Chemotaxonomic data revealed that the major fatty acids were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c; 26.7 %), C16:1 ω5c (18.9 %) and anteiso-C15:0 (12.9 %); the major polar lipid was identified as phosphatidylethanolamine; the polyamine pattern was found to contain sym-homospermidine; and the major quinone was identified as MK-7. The DNA-DNA relatedness of strain DG31A(T) with respect to H. arizonensis JCM 13504(T) was 19.5 ± 2.9 % (reciprocal, 19.3 ± 0.6 %). Based on these data, strain DG31A(T) should be classified within the genus Hymenobacter as a novel species for which the name Hymenobacter humi sp. nov. is proposed, with the type strain DG31A(T) (=KCTC 32523(T) = JCM 19635(T)).

Hymenobacter arcticus sp. nov., isolated from glacial till

A novel, red–pink-pigmented strain, designated R2-4T, was isolated from a till sample near Ny-Alesund, Svalbard Archipelago, Norway. Cells were aerobic, Gram-stain-negative and rod-shaped. Growth occurred at 4–30 °C (optimum, 20–22 °C), at pH 6.0–9.0 (optimum, pH 7.0) and with 0–1 % NaCl added to R2A agar. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R2-4T belonged to the genus Hymenobacter . 16S rRNA gene sequence similarity between strain R2-4T and the type strains of related species of the genus ranged from 94.51 to 96.05 %. Strain R2-4T contained iso-C15 : 0, anteiso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), summed feature 4 (C17 : 1 anteiso B and/or iso I) and C16 : 1ω5c as the major cellular fatty acids, MK-7 as the major respiratory quinone, and phosphatidylethanolamine, unknown aminophospholipids, unknown aminolipids and unknown lipids as the main polar lipids. The polyamine was sym-homospermidine. The DNA G+C content of strain R2-4T was 61.6 mol%. On the basis of phylogenetic, physiological and chemotaxonomic data, strain R2-4T is considered to represent a novel species of the genus Hymenobacter , for which the name Hymenobacter arcticus sp. nov. is proposed. The type strain is R2-4T ( = CCTCC AB 2012104T = KACC 16881T).

Hymenobacter qilianensis sp. nov., isolated from a subsurface sandstone sediment in the permafrost region of Qilian Mountains, China and emended description of the genus Hymenobacter

A red-pink, Gram-negative, rod-shaped, non-motile, non-spore-forming bacterium, designated strain DK6-37 was isolated from the permafrost region of Qilian Mountains in northwest of China. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that this isolate represents a novel member of the genus Hymenobacter, with low sequence similarities (<97 %) to recognized Hymenobacter species. Optimum growth was observed at 28 °C, pH 7.0 and 0 % NaCl. The strain was found to contain MK-7 as the predominant menaquinone. The polar lipids were identified as phosphatidylethanolanmine, two unknown aminophospholipids, one unknown aminolipid and three unknown polar lipids. The major fatty acids were identified as summed feature 3 (C16:1 ω7c/C16:1 ω6c as defined by MIDI), summed feature 4 (anteiso-C17:1 B/iso-C17:1 I), C16:1 ω5c, iso-C17:0 3-OH, iso-C15:0 and C18:0. The DNA G + C content was determined to be 67.4 mol %. On the basis of the polyphasic evidence presented, it is proposed that strain DK6-37 represents a novel species of the genus Hymenobacter, for which the name Hymenobacter qilianensis sp. nov. is proposed. The type strain is DK6-37(T) (= CGMCC 1.12720(T) = JCM 19763(T)).

Hymenobacter kanuolensis sp. nov., a novel radiation-resistant bacterium

A Gram-reaction-negative, rod-shaped, non-motile, red-pigmented, radiation-resistant, aerobic bacterium designated T-3(T) was isolated from a soil sample from the Qinghai-Tibet Plateau in Tibet, China, after exposure to 10 kGy gamma radiation. Phylogenetic analysis based on 16S rRNA sequences indicated that this isolate represented a novel member of the genus Hymenobacter. Sequence identities of the 16S rRNA gene of strain T-3(T) with the type strains of species of the genus Hymenobacter with validly published names range from 89% to 97%, and the most closely related species is Hymenobacter psychrotolerans Tibet-IIU11(T) (97%). The DNA-DNA relatedness between strain T-3(T) and H. psychrotolerans is 59.10%. The major fatty acids of strain T-3(T) were iso-C(15 : 0) (27.66%), summed feature 4 (iso-C(17 : 1)I and/or anteiso-C(17 : 1)B, 15.84%), anteiso-C(15 : 0) (14.08%) and summed feature 3 (C(16 : 1)ω7c and/or C(16 : 1)ω6c, 12.38%). The major menaquinone of strain T-3(T) was MK-7. Phosphatidylethanolamine (PE) was predominant in the polar lipid profile. The G+C content of the DNA of strain T-3(T) was 69.17 mol%. On the basis of the results of the polyphasic characterization presented in this study, it is concluded that strain T-3(T) represents a novel species of the genus Hymenobacter, for which the name Hymenobacter kanuolensis is proposed. The type strain is T-3(T) ( = ACCC 05760(T) = KCTC 32407(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, and these authors’ names will be included in the author index of the present issue. 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.