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This article contains an analysis of structural and functional parameters of bacterial complexes taken for examination from complete profiles of fens assigned to the Klyukvennoe and Karbyshevskoe wetlands in Tomsk oblast. Bacteria in the fens are revealed throughout the entire profile. Their number determined by a direct method of fluorescence microscopy is high and varies from 27 to 78 × 109 cells/g of dry peat. The high number of saprotrophic bacteria (to 108–109 CFU/g of dry peat) is detected by the plate method. An increase in the number of saprotrophic bacteria down the fen profile is revealed. These data enable us to conclude for the first time that index k (a dimensionless universal characteristic of natural prokaryotic communities) in fen profiles decreases with depth. The bacterial cultures isolated from the fens studied are assigned to ten taxa: Bacillus, Streptomyces, Arthrobacter, Microbacterium, Pseudomonas, Flavobacterium, Dyadobacter, Janthinobacterium, Pedobacter, and Myxobacteriales. The acrotelm is dominated by bacterial cultures represented by genera Bacillus and Streptomyces; and Pseudomonas, Dyadobacter, and Arthrobacter are the dominants of the catotelm. The functions of bacterial genera and species identified by molecular biological methods are described. The study of nitrogen fixation, denitrification, and methanogenesis has shown that bacteria are viable and active throughout the entire peat profile.

The study was conducted to comprehend the facets of culturable endophytic diversity correlating with the fitness of cultivar. Tomato bacterial endophytes from cultivars Arka Rakshak (AR; multi-disease tolerant hybrid) and Pusa Ruby (PR; susceptible check) were isolated. Molecular identification quantified that only two genera Rhizobium and Bacillus were common in both cultivars out of fifteen genera isolated. Genera Microbacterium, Enterobacter, Falsibacillus, Cohnella, Youhaiella, and Fluviicola were found only in AR, whereas genera Chryseobacterium, Pseudomonas, Dyadobacter, Staphylococcus, Micrococcus, Microvirga, and Shinella were found only in PR. Although the genera level diversity indicated cultivar specificity, except for firmicutes (7 in AR and 4 in PR), the distribution of taxonomic class alphaproteobacteria, gammaproteobacteria, bacteroidetes, and actinobacteria was almost similar. Gram-positive class was dominated by firmicutes and Gram-negative by alphaproteobacteria in both cultivars. On contrary, the collective functional profile for the production of hydrogen cyanide, ammonia, and siderophore, apart from phosphate solubilization and indole acetic acid production, indicated the dominance of endophytes from AR (multi-disease tolerant hybrid). The pattern of antagonistic ability against 15 different strains of R. solanacearum indicated that endophytes from tolerant cultivar exhibit higher in vitro suppression. The number of antagonists and the extent of inhibition both were higher in AR endophytes. However, the genetic capability for harboring eight antimicrobial compounds producing genes was found to be well distributed in both cultivars. Results showed that the functional aspects of these bacterial endophytes correlate with cultivar fitness more than that of taxonomic and genetic diversity.

A Gram-reaction-negative, yellow-pigmented, rod-shaped, aerobic, non-motile, non-spore-forming bacterium, designated strain QTA69T, was isolated from a subsurface sediment sample collected at the Qiangtang basin, Qinghai–Tibetan Plateau, PR China. Cells were catalase-positive and oxidase-negative. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain QTA69T was a member of the genus Dyadobacter and was closely related to Dyadobacter sediminis , Dyadobacter ginsengisoli and Dyadobacter psychrophilus with sequence similarities from 97.90 % to 96.85 %. Strain QTA69T grew at 4–35 °C, and the optimum temperature was 25–28 °C. It grew at the pH range of 6.0–9.0 (optimum, pH 7.0–8.0) and its NaCl tolerance was 0–2.0 % (optimum, 0–1.0 %). The major cellular fatty acids were summed feature 3 (iso-C15 : 0 2-OH and C 16:1ω6c/C16 : 1ω7c), iso-C15 : 0 and C16 : 1ω5c. The major respiratory quinone was MK-7 and the major polar lipid was phosphatidylethanolamine. Genome sequencing revealed a genome size of 8.41 Mbp and a G+C content of 46.87 mol%. Based on whole genome average nucleotide identity values, phenotypic data, phylogenetic data and genotypic data, strain QTA69T represents a novel species of genus Dyadobacter , for which the name Dyadobacter bucti sp. nov is proposed. The type strain is QTA69T (=CGMCC 1.13688T=KCTC 72024T).

The aim of this study was isolation and characterization of heterotrophic bacteria capable of ammonium and nitrite removal at 15 °C (optimal temperature for growing rainbow trout Oncorhynchus mykiss). Environmental isolates were grown in liquid media containing ammonium or nitrite, and best strains in terms of growth and ammonium or nitrite removal were identified via 16S rRNA sequencing. Dyadobacter sp. (no. 68) and Janthinobacterium sp. (no. 100) were selected for optimal adaptation to growth at 15 °C and best ammonium and nitrite removal (P P P

A novel bacterial strain, designated NS28T, was isolated from interfacial sediment sampled at Taihu Lake, PR China. Cells were rod-shaped, Gram-negative, aerobic and non-motile on Reasoner's 2A medium. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NS28T was most closely related to species from the genus Dyadobacter , with 98.4 and 96.0 % 16S rRNA gene sequence similarity to its closest phylogenetic neighbours Dyadobacter sediminis CGMCC 1.12895T and Dyadobacter luticola CCTCC AB 2017091T, respectively. MK-7 was the only cellular menaquinone. The major fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and C16 : 1ω5c. The major polar lipids were phosphatidylethanolamine, one phospholipid, one aminolipid, one lipid and two unidentified lipids. Genomic analysis of strain NS28T indicated that the total genome size was 6 477 094 bp with a G+C content of 44.8 mol%, 5380 protein-coding genes, 79 contigs and an N50 length of 299 584 bp. On the basis of the genomic DNA sequence, the average nucleotide identity values were 90.5 and 74.1 % with D. sediminis CGMCC 1.12895T and D. luticola CCTCC AB 2017091T, respectively. Digital DNA-DNA hybridization results of strain NS28T with D. sediminis CGMCC 1.12895T and D. luticola CCTCC AB 2017091T were 40.9 and 18.6 %, respectively. Based on the phenotypic, chemotaxonomic, phylogenetic and genome sequence data presented here, it is proposed that strain NS28T represents a novel species of the genus Dyadobacter for which the name Dyadobacter flavalbus is proposed . The type strain is NS28T (=NBRC 113854T=MCCC 1K03764T).

Four strains of bacteria designated as AR-3-6T, AT-3–1, AR-3-8T and AR-3–15 were isolated from Arctic soil. Cells were aerobic, Gram-staining-negative, non-motile, non-spore-forming, rod-shaped and yellow-pigmented. Flexirubin-type pigments were present in all strains. All strains tolerated 2 % of NaCl and were psychrotolerant. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that these strains formed a lineage within the family Cytophagaceae that were distinct from various members of the genus Dyadobacter . The closest member of strain AR-3-6T was D. koreensis DSM 19938T (97.2 % sequence similarity) and AR-3-8T was D. hamtensis HHS 11T (97.9 %). The predominant respiratory quinone was menaqinone-7. The major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. The DNA G+C content of strains ranges from 40.1 to 42.1 mol%. On the basis of phenotypic, genotypic, chemotaxonomic and phylogenetic analysis, both strains AR-3-6T and AR-3-8T represent a novel member in the genus Dyadobacter , for which the name Dyadobacter psychrotolerans sp. nov. and Dyadobacter frigoris sp. nov. are proposed, respectively. The type strain of Dyadobacter psychrotolerans is AR-3-6T (=KEMB 9005–743T=KACC 21172T=NBRC 113790T) and type strain of Dyadobacter frigoris is AR-3-8T (=KEMB 9005–744T= KACC 21173T=NBRC 113791T).

Strain Q3-56T, isolated from Arctic tundra soil, was found to be a Gram-stain-negative, yellow-pigmented, oxidase- and catalase-positive, non-motile, non-spore-forming, rod-shaped and aerobic bacterium. Strain Q3-56T grew optimally at pH 7.0 and 28 °C. The strain could tolerate up to 1 % (w/v) NaCl with optimum growth in the absence of NaCl. The strain was not sensitive to oxacillin and ceftazidime. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Q3-56T belonged to the genus Dyadobacter . Strain Q3-56T showed the highest sequence similarities to Dyadobacter luticola T17T (96.58 %), Dyadobacter ginsengisoli Gsoil 043T (96.50 %), Dyadobacter flavalbus NS28T (96.43 %) and Dyadobacter bucti QTA69T (96.43 %). The predominant respiratory isoprenoid quinone was identified as MK-7, The polar lipid profile of strain Q3-56T was found to contain one phosphatidylethanolamine, three unidentified aminolipids, three unidentified lipids and one unidentified phospholipid. The G+C content of the genomic DNA was determined to be 49.1 mol%. The main fatty acids were summed feature 3 (comprising C16 : 1 ω7c/C16 : 1 ω6c), iso-C15 : 0, C16 : 1 ω5c and iso-C16 : 1 3-OH. On the basis of the evidence presented in this study, a novel species of the genus Dyadobacter , Dyadobacter sandarakinus sp. nov., is proposed, with the type strain Q3-56T (=CCTCC AB 2019271T=KCTC 72739T). Emended descriptions of Dyadobacter alkalitolerans , Dyadobacter koreensis and Dyadobacter psychrophilus are also provided.

To investigate the effect of combined floating beds on nutrient removal under low temperature, an integrated floating bed with corn flakes (IFB-CF) and an integrated floating bed with light ceramsite (IFB-LC) were constructed in parallel. IFB-LC was used as control group under water temperatures of 9.3–14 °C and a water exchange time of 168 h. Nitrogen and phosphorus removal efficiency, the nutrient level of a hydrophyte (Oenanthe javanica), and the microbial population characteristics of the combined floating bed were investigated. For IFB-CF removal efficiencies, the degradation quantities of total nitrogen (TN), NO3−-N, and NH4+-N for IFB-CF were 13.58 ± 0.67 mg/L, 4.40 ± 0.61 mg/L, and 9.21 ± 0.38 mg/L, respectively; in contrast, degradation quantities for IFB-LC were lower (6.41 ± 1.47 mg/L, 2.15 ± 0.40 mg/L, and 5.95 ± 0.46 mg/L, respectively). The reductions in COD (Chemical Oxygen Demand, using K2Cr2O7 as oxidizer) for IFB-LC and IFB-CF were 86.89% and 66.06%, respectively. Using the MiSeq high throughput sequencing method, we analysed microbial community structure and diversity on the base material surface of the IFB-CF and IFB-LC. The results showed 15 phyla, 165 genera, and 78 families on the surface of the IFB-CF. The phylum, genus, and family with the highest abundances were Proteobacteria (48.29%), Trichococcus (10.39%), and Comamonadaceae (12.45%), respectively. We identified 15 phyla, 144 genera, and 93 families on the surface of the IFB-LC. The phylum, genus, and family with the highest abundances were Proteobacteria (46.10%), Dyadobacter (22.67%), and Cytophagaceae (28.75%), respectively. The Chao, ACE, and Shannon & Simpson indices for the IFB-LC were 4081, 6295, and 5.10, and 0.05, respectively; for the IFB-CF they were 4938, 7461, 5.77, and 0.02, respectively. Catalase (CAT) and Peroxidase (POD) concentrations in Oenanthe javanica for IFB-LC were 35.48 u/gFW/min and 1.03 u/gFW/min, respectively; for IFB-CF they were 32.33 u/gFW/min and 1.25 u/gFW/min, respectively. The nutritional energies of IFB-CF and IFB-LC were 107 kJ/100g and 84 kJ/100g. Using the Mondal model of TN removal, k (half-saturation constant) values for IFB-LC and IFB-CF were 35.67 mg/L and 39.23 mg/L, respectively, with a correlation coefficient (R2) of 0.97.

A Gram-stain-negative, aerobic, non-spore-forming, rod-shaped bacterial strain (UP-52T) was isolated from hydrocarbon-polluted groundwater located near an oil refinery in Tiszaujvaros, Hungary. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Dyadobacter in the family Cytophagaceae . Its closely related species are Dyadobacter frigoris (98.00 %), Dyadobacter koreensis (97.64 %), Dyadobacter psychrophilus (97.57 %), Dyadobacter ginsengisoli (97.56 %) and Dyadobacter psychrotolerans (97.20 %). The predominant fatty acids are summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω7c/C16 : 1 ω6c), C15 : 0 iso, C16 : 1 ω5c and C17 : 0 iso 3OH. The predominant respiratory quinone detected in strain UP-52T is quinone MK-7. The dominant polar lipids are glycolipid, phosphoaminolipid, phospholipid and aminolipid. The DNA G+C content is 40.0 mol%. Flexirubin-type pigment was present. Based on these phenotypic, chemotaxonomic and phylogenetic results, UP-52T represents a novel species of the genus Dyadobacter , for which the name Dyadobacter subterraneus sp. nov. is proposed. The type strain is UP-52T (=NCAIM B.02653T=CCM 9030T).

Here, we provide the complete genome sequence of the subsurface bacterial isolate Dyadobacter sp. strain NIV53, a candidate species from the Spirosomaceae family. The isolate contained one 7,587,604-bp chromosome, with a GC content of 40.4%, and one plasmid, pNIV1, with a size of 12,453 bp.

The objective of this study was to explore nitrogen removal, especially effluent dissolved organic nitrogen (DON) composition, relative genes and microbial community structures with four individual nitrogen sources at 5 °C. Results show that effluent DON did not have dependent relationship with the TN removal rate (urea > ammonia chloride > L -Alanine > D -Alanine). With the same influent TN, the highest effluent DON was formed with urea; the lowest DON was fed with ammonia chloride. The main DON composition was the product of cell metabolism excluding urea, rather than the original substrate. Glutamic acid synthesizing process was of great importance to DON accumulation at 5 °C. The nitrogen source type was important to the diversity and heterogeneity of the nitrogen removal genes. Bacterial population structure using redundancy analysis (RDA) showed Simplicispira occupied a higher abundance remarkably in the reactors feeding with urea, and Dyadobacter occupied higher feeding with l -Alanine.

The native bacterial populations present in three brands of Spring Mix salads (brands A, B, and C) were analyzed by plating and 16S rRNA gene sequencing during 15 days of storage at 4 °C. While the traditional plating method did not show significant differences among three brands or between before and after storage, 16S rRNA gene sequencing showed that the “brand” factor significantly impacted the diversity and abundance of native bacterial populations. In order to evaluate the interaction between native bacteria and Escherichia coli O157:H7 (ECO157), day-0 and day-15 salad homogenates were inoculated with ECO157 (a final concentration of 5.5 log CFU/ml). Inoculated samples were stored at 4 °C for additional 15 days and the behavior of inoculated ECO157 was monitored by plating samples on CHROMagar™ O157 agar on days 0, 5, 10 and 15. The top four phyla of bacteria present in all three brands of salad were Proteobacteria, Bacterioidetes, Actinobacteria, and Firmicutes. Changes in the relative abundance and diversity of bacterial populations were significantly altered by inoculation of ECO157. The inoculation remarkably decreased the beta diversity (Jaccard distance) of the bacterial populations (P = 0.005). During the additional 15-day storage, culturable ECO157 cells decreased over the entire storage time. However, fluctuations of culturable ECO157 cells were observed on days 5 and 10. In day-0 brand A and day-15 brands A and C, culturable ECO157 cells were significantly higher on day 10 than on day 5. Microbiome analysis results showed that the relative abundance of Planomicrobium, Aeromonas, Carnobacterium, and Fusobacterium were negatively correlated with the decreasing numbers of culturable ECO157 cells from day 5 to day 10 after inoculation and the relative abundance of genera Methylotenera, Yersinia, Shewanella, Dyadobacter, and Brochothrix were positively correlated with the increasing numbers of culturable ECO157 cells from day 5 to day 10. This study provides in-depth information on the microbiome changes in bagged salad and their impact on food safety, which can assist with the risk assessment of produce products of different shelf life and facilitate the development of new intervention strategies for protecting the microbial safety of fresh produce.

Novel sialic acid scaffolds have great significance in the development of influenza neuraminidase inhibitors. Here the enzymatic synthesis of a wide range of 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid (KDN) analogues via aldol addition of pyruvate to D-mannose, D-glucose, D-galactose, 2-deoxy-D-glucose, D-arabinose, L-arabinose and L-rhamnose using a previously unstudied N-acetylneuraminic acid (Neu5Ac) aldolase derived from the bacterium Dyadobacter fermentas was exemplified. Several of the synthesized KDN analogues showed comparable or better inhibitory activity than unstudied Neu5Ac against the mutated influenza neuraminidases (A/California/04/2009 and A/Anhui/1/2005), which both show resistance to Neu5Ac-based neuraminidase inhibitors, demonstrating that these compounds are promising templates for the development of anti-influenza drugs.

Bacteria have been shown to be involved in different species-specific interactions with eukaryotic algae such as diatoms, impacting important ecosystem processes. Recently, a strain assigned to Dyadobacter, named ‘species 32’, has been shown to be involved in a number of ecologically relevant diatom processes, such as biofilm formation or growth enhancement, depending on the diatom species. This bacterium was originally isolated from a culture of freshwater benthic diatoms that originated from an epilithic biofilm, in which both bacteria and diatoms coexist. A single complete circular chromosome of Dyadobacter sp. 32 was assembled with a length of 7,101,228 bp, containing 6062 protein coding genes and 3 rRNA operons. A number of interesting genetic features were found, such as a putative zeaxanthin biosynthetic gene cluster. A large number of polysaccharide utilizing gene clusters were also detected, along with genes potentially acquired from other bacteria through horizontal gene transfer, and genes previously identified in other algae-bacteria interactions. These data serve to increase our understanding of specific interactions within freshwater biofilms, and identify a number of gene targets with which to study the molecular basis of diatom-bacteria interactions. published

Glaciers have been recognized as biomes, dominated by microbial life. Many novel species have been isolated from glacier ecosystems, and their physiological features are well characterized. However, genomic features of bacteria isolated from the deep ice core are poorly understood. In this study, we performed a comparative genomic analysis to uncover the genomic features of strain Dyadobacter tibetensis Y620-1 isolated from a 59 m depth of the ice core drilled from a Tibetan Plateau glacier. Strain D. tibetensis Y620-1 had the smallest genome among the 12 cultured Dyadobacter strains, relatively low GC content, and was placed at the root position of the phylogenomic tree. The gene family based on a nonmetric multidimensional scaling (NMDS) plot revealed a clear separation of strain D. tibetensis Y620-1 from the reference strains. The genome of the deep ice core isolated strain contained the highest percentage of new genes. The definitive difference is that all genes required for the serine-glyoxylate cycle in one-carbon metabolism were only found in strain D. tibetensis Y620-1, but not in any of the reference strains. The placement of strain D. tibetensis Y620-1 in the root of the phylogenomic tree suggests that these new genes and functions are of ancient origin. All of these genomic features may contribute to the survival of D. tibetensis Y620-1 in the glacier.

A Gram-stain-negative, non-motile, aerobic bacterial strain, designated T17T was isolated from a sample of sewage sediment from a Busan park (Republic of Korea). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain T17T had the highest 16S rRNA gene sequence similarity to Dyadobacter soli KCTC 22481T (97.3 %), D.yadobacter fermentans DSM 18053T (97.1 %) and D.yadobacter sediminis CGMCC 1.12895T (97.1 %). The isolate exhibited relatively low levels of DNA–DNA relatedness with respect to D. soli KCTC 22481T (28.2±3.6 %). The DNA G+C content was 49.1 mol%. The unique respiratory quinone was MK-7 and the major polar lipids were phosphatidylethanolamine, five unidentified lipids, four aminolipids, two unidentified phospholipids and one glycophospholipid. The predominant cellular fatty acids (>5 % of total) were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH; 44.3 %), iso-C15 : 0 (15.7 %), C16 : 1 ω5c (9.6 %), iso-C17 : 0 3-OH (9.3 %) and C16 : 0 (5.6 %). Moreover, physiological and biochemical characteristics distinguished strain T17T from its related species, including temperature and pH ranges for growth, being positive for acetate hydrolysis, and being negative for acid produced from melibiose and rhamnose. The genotypic, chemotaxonomic and phenotypic data revealed that strain T17T represents a novel species of the genus Dyadobacter , for which the name Dyadobacter luticola sp. nov. is proposed. The type strain is T17T (=KCTC 52981T=CCTCC AB 2017091T).

Three biodegradation were carried out in soils with activator, non-activator and no activator. For oil-addicted biodegradation, macro-alkanes were devoured (soil S1:3313 mg C18-C30/kg, soil S2: 2741 mg C18-C30/kg) in soils with activator, which was 3.8 times of that for non-oil-addicted biodegradation. For oil-addicted biodegradation, high respiratory activity (S1: 0.8 CO2/kg soil, S2: 0.6 mg CO2/kg soil) and rapid growth rate (S1: 48 %, S2: 36 %) of oil-addicted microbe with activator were observed. Moreover, for oil-addicted biodegradation, low consumption of NH4+-N (22 mg/kg) and acetic acid (410 mg/kg) were observed, which were 1/8 and 4/5 for non-oil-addicted biodegradation. Meanwhile, rapid growth and high respiratory activity of the genera Pseudomonas, Diaminobutyricimonas, Dyadobacter and Galbitalea were observed. It indicated that macro-alkanes instead of organic matter such as aromatic protein I and II, fulvic acid-like, soluble microbial metabolites, humic acid-like was utilized rapidly for oil-addicted biodegradation due to less consumption of NH4+-N and acetic acid.

Dissolved organic matter (DOM) released from biochar can influence the microbial community structure, but the inherent mechanism associated with the structure of biochar-derived DOM remains insufficiently elucidated. In this study, the spectroscopic characteristics and molecular structures of biochar-derived DOM were studied, and the microbial responses to biochar-derived DOM were explored. With increasing biochar pyrolysis temperature (PT), the molecular weight and proportions of aliphatic and fulvic acid-like compounds in the biochar-derived DOM decrease along with an reduction in the amount of DOM released from the biochars, but the proportions of combustion-derived condensed polycyclic aromatics and humic acid-like and soluble microbial byproduct-like compounds increased. Accordingly, the humification index, H/C and (O + N)/C values also decreased. The spectroscopic characteristics of biochar-derived DOM were distinct from those of natural substrates. Moreover, the DOM extracted from biochar raw materials contained a high proportion of aliphatic compounds, while the DOM derived from high-PT biochars (500 °C) had similar characteristics to fulvic acid-like and soluble microbial byproduct-like compounds. The microbial abundance and community structure varied in different DOM solutions. The relative abundances (RAs) of eight genera (e.g. Dyadobacter, Sphingobacterium and Novosphingobium) had significantly positive correlations with the content of aliphatic compounds, while RAs of seven genera (e.g. Methylotenera, Acinetobacter and Reyranella) had significant positive correlations with the content of high-aromatic combustion-derived condensed polycyclic aromatics. These results are helpful for obtaining a deep understanding of the potential influences of various types of biochar-derived DOM on terrestrial and aquatic microbiology.

Two strains of bacteria designated strains S-53T and A27T were isolated from forest soil and subjected to polyphasic characterization. Cells were aerobic, Gram-staining-negative, catalase- and oxidase- positive, non-motile, non-spore-forming, rod-shaped, and yellow-pigmented. Flexirubin-type pigments were present. Both strains were positive for PNPG, hydrolysed casein, and tyrosine. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strains S-53T and A27T formed a lineage within the family Cytophagaceae that were distinct from various members of the genus Dyadobacter (98.9–93.2% sequence similarity). Closest member for strain S-53T was Dyadobacter jejuensis AM1R11T (95.7%) and for A27T Dyadobacter endophyticus 65T (98.9%). The predominant respiratory quinone was MK-7 for both strains. The major polar lipid for both strains was phosphatidylethanolamine. The major cellular fatty acids for both strains were summed feature 3 (C16:1ω7c and/or C16:1ω6c), iso-C15:0, C16:1ω5c, and C16:0. The DNA G+C content of strains ranges from 46.5 to 48.7 mol%. On the basis of phenotypic, genotypic, chemotaxonomic, and phylogenetic analysis, both strains S-53T and A27T represent a novel member in the genus Dyadobacter, for which the name Dyadobacter flavus sp. nov. and Dyadobacter terricola sp. nov. are proposed, respectively. The type strain of D. flavus is S-53T (= KEMB 9005-541T = KACC 19149T = NBRC 112681T) and type strain of D. terricola is A27T (= KEMB 9005-524T = KACC 19147T = NBRC 112680T).

The existence of multiple-antibiotic-resistant strains of environmental bacteria is commonly linked to human activities. However, multiple-antibiotic-resistant strains of bacteria are also widely found in the Antarctic that has limited human activity. This study was conducted to examine the prevalence of antibiotic-resistant strains among Antarctic bacteria. Forty-five bacterial strains from Estrellas lake of King George Island and Crater lake of Deception Island, Antarctic, were exposed to 30 different antibiotics. Forty out of the 45 bacterial strains were affiliated to 12 genera, Aeromicrobium, Arthrobacter, Bacillus, Brevundimonas, Cryobacterium, Dyadobacter, Flavobacterium, Methylibium, Pedobacter, Pseudomonas, Rhodococcus, and Sphingomonas. Among the bacteria, 43 strains were resistant to at least three antibiotics, and 26 strains were resistant to 10 or more different antibiotics. Pseudomonas spp. and four unknown Microbacteriaceae bacteria were found to be resistant to majority of the antibiotics tested. Two bacteria, each from Estrellas and Crater lakes, were sensitive to all the antibiotics tested. These results indicated that Antarctic bacteria are probably the reservoirs for antibiotic resistance genes.

The threat of climate change has intensified efforts toward the development of safer alternatives to depleting fossil fuels (Cox et al., 2000). Lignocellulosic bioethanol is considered to be a viable and environmentally friendly alternative to fossil fuels. Though lignocellulosic biomass is available in massive quantities and is renewable (Dillon and Dillon, 2003; Lynd et al., 2008; Pauly and Keegstra, 2008; Kricka et al., 2015), the presence of certain barriers makes lignocellulosic bioethanol expensive. Discovery of proteins with novel specificities is necessary to break these barriers and make lignocellulosic bioethanol economically viable (Horn et al., 2012; Ulaganathan et al., 2015). Cellulolytic bacteria isolated from various environments have been explored for proteins of potential use in lignocellulosic bioethanol production (Badger, 2002; Wang et al., 2012; Pinheiro et al., 2015). Bacteria belonging to the genera Bacillus, Bacteroides, Butyrivibrio, Cellulosimicrobium, Citrobacter, Clostridium, Devosia, Dyadobacter, Ensifer, Kaistia, Labrys, Methanobrevibacter, Microbacterium, Ochrobactrum, Paracoccus, Pseudomonas, Rhizobium, Ruminococcus, Shinella, Siphonobacter, Stenotrophomonas, Trichonympha, and Variovorax, were found to be cellulolytic (Saxena et al., 1993; Schwarz, 2001; Gupta et al., 2012; Huang et al., 2012; Yanga et al., 2014). Bacillus pumilus strains are known to produce cellulase enzyme up to a maximum of 11.4 mg/g of cell dry mass (Suzuki and Kaneko, 1976; Kotchoni and Shonukan, 2002; Ariffin et al., 2006). The cellulase enzyme produced by B. pumilus strain EB3 has been found to be superior to fungal cellulases due to its higher optimum pH and temperature (Ariffin et al., 2006). Further it has been shown that the B. pumilus cellulase enzyme could be mutated to remove the catabolite repression (Kotchoni et al., 2003). We have recently isolated bacterial strains from the gut contents of the wood boring Mesomorphus sp. These isolates were screened for cellulolytic and xylose isomerase activities and the isolate ku-bf1 which exhibited maximum cellulolytic and xylose isomerase activities was identified as B. pumilus by 16S rRNA sequencing. The whole genome of this strain has been sequenced. The dataset has been submitted to NCBI and is reported here.

A pink-pigmented, gram-negative, non-motile, non-gliding, flexirubin-negative, rod-shaped and strictly aerobic bacterial strain, designated PTR3T, was isolated from a soil sample from Goyang, South Korea. Growth occurred between 10 and 42 °C (optimum 30 °C), 0–4 % (w/v) NaCl (optimum 0 %) and pH 6–9 (optimum 7–8). Phylogenetic analysis based on 16S rRNA sequences showed that strain PTR3T forms a distinct clade with type strains of the closely related genus, Dyadobacter, with similarities of 93.6 and 91.3–93.6 %, respectively. The strain produces a pink carotenoid pigment(s). The major polar lipids are an unidentified aminophospholipid and an aminolipid. Strain PTR3T was found to contain MK-7 as the predominant menaquinone and C16:1 ω7c and/or C16:1 ω6c as the major fatty acids. The DNA G + C content of strain PTR3T was deterrmined to be 45.9 mol %. Based on the chemotaxonomic, phylogenetic and other physiological properties, strain PTR3T (=KCTC 42819T = JCM 31133T) is concluded to represent a novel species in a new genus within the family Cytophagaceae, for which the name Telluribacter humicola gen nov., sp. nov., is proposed.

A Gram-negative, aerobic bacterium, designated strain BZ26T, was isolated from hydrocarbon-contaminated soil. The strain was psychrophilic, showing good growth over a temperature range of 1–20 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ26T was related to members of the genus Dyadobacter and had highest 16S rRNA gene sequence similarity to Dyadobacter alkalitolerans 12116T (98.1 %), Dyadobacter koreensis KCTC 12537T (97.5 %) and Dyadobacter ginsengisoli Gsoil 043T (97.2 %). Strain BZ26T had MK-7 as the major menaquinone and summed feature 3 (C16 : 1 ω7c/iso-C15 : 0 2-OH), C16 : 1 ω5c and iso-C15 : 0 as major fatty acids. The genomic DNA G+C content of strain BZ26T was 48.9 mol%. On the basis of phenotypic characteristics and genotypic analysis, strain BZ26T is considered to represent a novel species of the genus Dyadobacter, for which the name Dyadobacter psychrophilus sp. nov. is proposed. The type strain is BZ26T (=DSM 22270T =CGMCC 1.8951T).

An aerobic, Gram-stain-negative, oxidase- and catalase-positive, non-motile, non-spore-forming, rod-shaped, pink-pigmented bacterium, designated strain R49T, was isolated from soil. Flexirubin-type pigments were absent. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain R49T formed a lineage within the family Cytophagaceae of the phylum Bacteroidetes that was distinct from the most closely related genera Dyadobacter (91.98-93.85 % sequence similarity), Persicitalea (88.69 %) and Runella (84.79-85.81 %). The major isoprenoid quinone was menaquinone-7 (MK-7) and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0, C16 : 1ω5c, C16 : 0 and iso-C17 : 0 3-OH. The DNA G+C content of strain R49T was 53.9 mol%. On the basis of phenotypic, genotypic and phylogenetic analysis, strain R49T represents a novel species of a new genus in the family Cytophagaceae, for which the name Rhabdobacter roseus gen. nov., sp. nov. is proposed. The type strain of Rhabdobacter roseus is R49T ( = KEMB 9005-318T = KACC 18395T = JCM 30685T).

A Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacterium, strain Gsoil 043T, was isolated from soil from a ginseng field in Pocheon province, South Korea. The novel isolate was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 043T was shown to belong to the family ‘Flexibacteraceae’ and was related to Dyadobacter fermentans (96.7 %), Dyadobacter crusticola (96.3 %) and Dyadobacter hamtensis (95.8 %). The 16S rRNA gene sequence similarity of the novel strain to other recognized species within the family ‘Flexibacteraceae’ was less than 87.0 %. The G+C content of genomic DNA was 48 mol%. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; major fatty acids, C16 : 1 ω7c, iso-C15 : 0 and C16 : 0) supported the affiliation of strain Gsoil 043T to the genus Dyadobacter. The results of physiological and biochemical tests enabled strain Gsoil 043T to be differentiated genotypically and phenotypically from the three Dyadobacter species with validly published names. The novel isolate therefore represents a novel species for which the name Dyadobacter ginsengisoli sp. nov. is proposed, with the type strain Gsoil 043T (=KCTC 12589T=LMG 23409T).

Bacterial strain CP183-8T was isolated from biological soil crusts collected in the Colorado Plateau, USA. Cells of this strain were aerobic, non-motile, Gram-negative, psychrotolerant and formed beaded chains in the stationary growth phase. They contained C16 : 1 ω5c and C16 : 1 ω7c as major fatty acids. 16S rRNA gene sequence analysis assigned the strain to the genus Dyadobacter. However, it shared a sequence similarity of only 95·88 % with the type strain of Dyadobacter fermentans, NS114T. Because it also exhibited a significant number of phenotypic and chemotaxonomic differences from D. fermentans, it is described as a novel second species in the genus Dyadobacter, with the name Dyadobacter crusticola sp. nov. The type strain is CP183-8T (=DSM 16708T=ATCC BAA-1036T).

Dyadobacter tibetensis Y620-1 is the type strain of the species Dyadobacter tibetensis, isolated from ice at a depth of 59 m from a high altitude glacier in China (5670 m above sea level). It is psychrotolerant with growth temperature ranges of 4 to 35°C. Here we describe the features of this organism, together with the draft genome sequence and annotation. The 5,313,963 bp long genome contains 4,828 protein-coding genes and 39 RNA genes. To the best of our knowledge, this is the first Dyadobacter strain that was isolated from glacial ice. This study provides genetic information of this organism to identify the genes linked to its specific mechanisms for adaption to extreme glacial environment.

A Gram-negative bacterium, designated NS114T, was isolated from duplicate treatments of surface-sterilized Zea mays stems. The plants were grown in synthetic soil under greenhouse conditions and watered with fertilizer containing no nitrogen. Strain NS114T could not be isolated from plants watered with the standard level or 20% (w/v) of the standard level of nitrogen. Cells occurred as pairs in young cultures that attached to form angled arrangements in R2A broth and occasionally formed rounded, horseshoe arrangements in YM broth. Cell variation resulted in flocculent chains of coccoid cells in old cultures. Strain NS114T fermented glucose and sucrose. The G + C content was 48 mol%. Phylogenetic analysis of the 16S rRNA gene showed that the strain was a member of the domain Bacteria and branched from a point equidistant from an aquatic organism, Runella slithyformis and a marine isolate, 'Microscilla furvescens'. Phenotypic and genotypic analyses indicated that strain NS114T could not be assigned to any recognized genus; therefore a new genus and species, Dyadobacter fermentans gen. nov., sp. nov., is proposed, for which NS114T is the type strain.

A non-motile, rod-shaped, light-yellow-pigmented bacterium, designated strain WPCB159T, was isolated from freshwater samples collected from the Woopo wetland in Korea. The cells were Gram-negative, aerobic and catalase- and oxidase-positive. The major fatty acids were C16 : 1 ω7c (34.8 %), iso-C15 : 0 (24.2 %) and C16 : 0 (9.4 %). The DNA G+C content was 44 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain WPCB159T forms a lineage within the genus Dyadobacter (family ‘Flexibacteraceae’) and is closely related to Dyadobacter hamtensis HHS 11T (97.8 % sequence similarity) and to other members of the genus Dyadobacter (95.2–96.8 % sequence similarity). The phenotypic characteristics and DNA–DNA hybridization relatedness data indicate that strain WPCB159T should be distinguished from D. hamtensis HHS 11T. On the basis of the evidence presented in this study, strain WPCB159T represents a novel species of the genus Dyadobacter, for which the name Dyadobacter koreensis sp. nov. is proposed. The type strain is WPCB159T (=KCTC 12537T=NBRC 101116T).

Twenty samples were taken from the inner or outer surfaces of stone monuments of six historic Scottish buildings and ruins. Biofilms developing on mineral substrates were analysed by in situ scanning electron microscopy and cultivation. Various methods were used to characterize the isolates including automated ribotyping, RAPD and sequencing of the 16S rRNA gene for bacteria, and stereomicroscopy and sequencing of the Internal Transcribed Spacers (ITS) for fungi. Most samples contained microbes between 10(5) and 10(7)cfug(-1) substrate. Actinobacteria belonging to the genus Streptomyces (17 samples/5 monuments) or Arthrobacter (12/3) and Pseudomonas (9/3) were frequently detected. Most streptomycetes were in terms of their 16S rRNA gene sequence most closely related to S. microflavus (10/3) or to the undescribed species S. "vulgaris" (8/3). Indoor and outdoor biofilms exhibited significant differences in their microbiota, as shown by both microscopy and isolation studies. Pigmented coccoid Arthrobacter species were typical for the outdoor samples, whereas Pseudomonas species were common in the indoor samples. Based on the low phylogenetic relationship to a known species (type strain), potential novel pigmented bacterial species belonging to the genera Arthrobacter, Brevundimonas, Cryseobacterium, Deinococcus and Dyadobacter were detected from the outdoor samples and to Pseudomonas from the indoor samples. Hyaline fungal species of Acremonium (10/4) mainly occurred in indoor samples, whereas pigmented species of Cladosporium (8/3), Penicillium (6/3) and Phialophora (6/2) were found outdoors. Using in situ microscopy diatom algae were also detected.

Strain HHS 11T was isolated from a water sample collected from the snout of Hamta glacier located in the Himalayan mountain ranges of India. Phenotypic, chemotaxonomic and phylogenetic analyses established the affiliation of the isolate to the genus Dyadobacter. HHS 11T possessed 96 and 95 % 16S rRNA gene sequence similarity with respect to Dyadobacter crusticola and Dyadobacter fermentans, respectively. Furthermore, strain HHS 11T differs from D. crusticola and D. fermentans in a number of phenotypic characteristics. These data suggest that strain HHS 11T represents a novel species of the genus Dyadobacter, for which the name Dyadobacter hamtensis sp. nov. is proposed. The type strain is HHS 11T (=JCM 12919T=MTCC 7023T).

This study aimed to investigate whether the presence of trichomes as conspicuous physical attributes of the leaf surface affects the microbial community composition on Arabidopsis thaliana leaves. The A. thaliana ecotype Col-0 and its trichomeless gl1 mutant were grown in growth cabinets under climate-controlled conditions. The gl1 mutant showed a similar wax composition as the Col-0 wild type with slightly reduced amounts of C(29), C(31) and C(33) alkanes by GC/MS and GC/FID analyses. 120 bacterial isolates representing 39 bacterial genera were obtained from A. thaliana Col-0 leaf surfaces. Phylogenetic analysis of nearly full-length 16S rRNA sequences from 29 selected isolates confirmed their affiliation to the Proteobacteria (Alpha-, Beta-, Gamma-), Actinobacteria, Bacteroidetes and Firmicutes. The bacterial diversity on A. thaliana ecotype Col-0 and its gl1 mutant, devoid of trichomes, were further compared by denaturing gradient gel electrophoresis (DGGE). Banding patterns and sequencing of representative DGGE bands revealed the presence of phylotypes related to Sphingomonas (Alphaproteobacteria), Methylophilus (Betaproteobacteria) and Dyadobacter (Bacteroidetes) which are common phyllosphere inhabitants. Furthermore, wildtype and trichomeless mutant plants were exposed to outdoor conditions for 4-5 weeks. The DGGE gels showed only minor differences between the two plant lines, thus suggesting that trichomes per se do not affect bacterial diversity on Arabidopsis leaves under the experimental conditions tested.