Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species

The pink-pigmented facultative methylotrophs (PPFMs), a major bacterial group found in the plant phyllosphere, comprise two genera: Methylobacterium and Methylorubrum. They have been separated into three major clades: A, B (Methylorubrum), and C. Within these genera, however, some species lack either pigmentation or methylotrophy, which raises the question of what actually defines the PPFMs. The present study employed a comprehensive comparative genomics approach to reveal the phylogenetic relationship among the PPFMs and to explain the genotypic differences that confer their different phenotypes. We newly sequenced the genomes of 29 relevant-type strains to complete a dataset for almost all validly published species in the genera. Through comparative analysis, we revealed that methylotrophy, nitrate utilization, and anoxygenic photosynthesis are hallmarks differentiating the PPFMs from the other Methylobacteriaceae. The Methylobacterium species in clade A, including the type species Methylobacterium organophilum, were phylogenetically classified into six subclades, each possessing relatively high genomic homology and shared phenotypic characteristics. One of these subclades is phylogenetically close to Methylorubrum species; this finding led us to reunite the two genera into a single genus Methylobacterium. Clade C, meanwhile, is composed of phylogenetically distinct species that share relatively higher percent G+C content and larger genome sizes, including larger numbers of secondary metabolite clusters. Most species of clade C and some of clade A have the glutathione-dependent pathway for formaldehyde oxidation in addition to the H4MPT pathway. Some species cannot utilize methanol due to their lack of MxaF-type methanol dehydrogenase (MDH), but most harbor an XoxF-type MDH that enables growth on methanol in the presence of lanthanum. The genomes of PPFMs encode between two and seven (average 3.7) genes for pyrroloquinoline quinone-dependent alcohol dehydrogenases, and their phylogeny is distinctly correlated with their genomic phylogeny. All PPFMs were capable of synthesizing auxin and did not induce any immune response in rice cells. Other phenotypes including sugar utilization, antibiotic resistance, and antifungal activity correlated with their phylogenetic relationship. This study provides the first inclusive genotypic insight into the phylogeny and phenotypes of PPFMs

High-Throughput Identification and Screening of Novel Methylobacterium Species Using Whole-Cell MALDI-TOF/MS Analysis

Methylobacterium species are ubiquitous α-proteobacteria that reside in the phyllosphere and are fed by methanol that is emitted from plants. In this study, we applied whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis (WC-MS) to evaluate the diversity of Methylobacterium species collected from a variety of plants. The WC-MS spectrum was reproducible through two weeks of cultivation on different media. WC-MS spectrum peaks of M. extorquens strain AM1 cells were attributed to ribosomal proteins, but those were not were also found. We developed a simple method for rapid identification based on spectra similarity. Using all available type strains of Methylobacterium species, the method provided a certain threshold similarity value for species-level discrimination, although the genus contains some type strains that could not be easily discriminated solely by 16S rRNA gene sequence similarity. Next, we evaluated the WC-MS data of approximately 200 methylotrophs isolated from various plants with MALDI Biotyper software (Bruker Daltonics). Isolates representing each cluster were further identified by 16S rRNA gene sequencing. In most cases, the identification by WC-MS matched that by sequencing, and isolates with unique spectra represented possible novel species. The strains belonging to M. extorquens, M. adhaesivum, M. marchantiae, M. komagatae, M. brachiatum, M. radiotolerans, and novel lineages close to M. adhaesivum, many of which were isolated from bryophytes, were found to be the most frequent phyllospheric colonizers. The WC-MS technique provides emerging high-throughputness in the identification of known/novel species of bacteria, enabling the selection of novel species in a library and identification without 16S rRNA gene sequencing

Harvest and postharvest quality of sweet cherry are improved by pre-harvest benzyladenine and benzyladenine plus gibberellin applications

This study was carried out to evaluate the effects of pre-harvest benzyladenine (BA) and BA plus gibberellin (GA4+7) treatments on fruit quality attributes of ‘0900 Ziraat’ cherry at harvest and after cold storage. ‘0900 Ziraat’ cherry trees were sprayed with BA (50, 100, and 150 mg·L–1) and BA + GA4+7 (12.5, 25, and 50 mg·L–1) when fruit was at their straw-yellow color stage. All of the treated fruit were significantly firmer than control fruit. Fruit treated with 25 and 50 mg·L–1 BA + GA4+7 and 50 and 150 mg·L–1 BA had significantly higher soluble solids content (SSC) than untreated fruit. Sweet cherry trees treated with the optimum concentration of BA + GA4+7 (50 mg·L–1) yielded fruit with 15.17 % greater weight, 9.0 % higher firmness and 13.6 % higher SSC. Additional samples were harvested, placed in plastic bags, and stored at 4 °C for 30 days. At the end of the cold storage period, fruit treated with 25 and 50 mg·L–1 BA + GA4+7 and 50 and 150 mg·L–1 BA were significantly firmer than the control. 50 mg·L–1 BA + GA4+7 -treated fruit had higher SSC than untreated ones.  In conclusion, fruit treated with the optimum dose of BA + GA4+7 (50 mg·L–1) were larger and firmer than untreated fruit at harvest and this concentration had the best effects. Most of the treated fruit maintained a superior firmness and quality to control fruit during cold storage

Microflora On The Skin Of European Eel (Anguilla Anguilla L., 1758) Sampled From Creek Yuvarlakçay, Turkey

Bacterial skin microflora of eel obtained from Mugla (Turkey) province were studied. The aero- bic bacteria associated with skin and slime were estimated using the dilution plate technique. The dominant bacterial species were Pseudomonas spp. (17.23%), Acinetobacter baumannii (15.51%) and Stenotrophomonas maltophilia (12.05%). A lower frequency of Gram-positive bacteria (18.93%) was found in samples

Use of Heteroatom-Doped g-C3N4 Particles as Catalysts for Dehydrogenation of Sodium Borohydride in Methanol

Here, graphitic carbon nitride (g-C3N4) was synthesized from melamine, doped with heteroatoms, such as B, S, and P reported using boric acid, sulfur, and phosphorous red as dopants, respectively. The catalytic performances of g-C3N4, and heteroatom-doped g-C3N4 (H@g-C3N4 (H=B, S or P) particles as catalysts in the dehydrogenation of sodium borohydride (NaBH4) in methanol to generate hydrogen (H2) were investigated. The prepared g-C3N4-based structures were used as catalysts for hydrogen (H2) production in the dehydrogenation reaction of sodium borohydride (NaBH4) in methanol. The catalytic performance of H@g-C3N4 (H=B, S or P) structures in the dehydrogenation reaction of sodium borohydride (NaBH4) in methanol was determined to be higher than the catalytic performance of the bare g-C3N4 structure. The hydrogen generation rate (HGR) values were calculated for the reactions catalyzed by B@g-C3N4, P@g-C3N4, and S@g-C3N4 as 609 ± 48, 699 ± 48, and 429 ± 55 mL H2/g of cat.min, respectively, which is only 282 ± 11 mL H2/g of cat.min for the native g-C3N4-catalyzed one. The activation energies (Ea) were found to be relatively low, such as 31.2, 26.9, and 31.2 kJ/mol, for the reactions catalyzed by B@g-C3N4, P@g-C3N4, and S@g-C3N4, respectively. In addition, in the reuse studies, it was concluded that B@g-C3N4, P@g-C3N4, and S@g-C3N4 catalysts can readily complete the reaction with 100% conversion, even in five consecutive uses, and afforded promising potential with more than 80% activity for each use

Teachers’ Sensitivity towards Technology and Environmental Ethics

The purpose of the current study was to determine the science and classroom teachers’ ethical sensitivities towards the issues of technology and the environment. Thus, the current study was conducted on 239 science and classroom teachers. The study employed the mixed method, in which qualitative and quantitative methods are used together. The quantitative dimension of the study is comprised of a survey, which was developed by the researchers. The qualitative dimension of the study comprised of three scenarios created by the researchers. Two of these scenarios are related to the environment and the other one is related to biotechnology. As a result of the study, the teachers’ ethical sensitivities towards technology and environmental issues were found to be high. For some items in the questionnaire significant differences in gender-based, branch-based, and professional experience were found. The results obtained from the scenarios revealed that while science teachers adapt more realistic approaches to the events, the classroom teachers make decisions for the future. It would be useful to organize in-service training and ethical awareness training for teachers who are in the beginning of their professional lives

Use of Heteroatom-Doped g-C₃N₄ Particles as Catalysts for Dehydrogenation of Sodium Borohydride in Methanol

Here, graphitic carbon nitride (g-C3N4) was synthesized from melamine, doped with heteroatoms, such as B, S, and P reported using boric acid, sulfur, and phosphorous red as dopants, respectively. The catalytic performances of g-C3N4, and heteroatom-doped g-C3N4 (H@g-C3N4 (H=B, S or P) particles as catalysts in the dehydrogenation of sodium borohydride (NaBH4) in methanol to generate hydrogen (H2) were investigated. The prepared g-C3N4-based structures were used as catalysts for hydrogen (H2) production in the dehydrogenation reaction of sodium borohydride (NaBH4) in methanol. The catalytic performance of H@g-C3N4 (H=B, S or P) structures in the dehydrogenation reaction of sodium borohydride (NaBH4) in methanol was determined to be higher than the catalytic performance of the bare g-C3N4 structure. The hydrogen generation rate (HGR) values were calculated for the reactions catalyzed by B@g-C3N4, P@g-C3N4, and S@g-C3N4 as 609 ± 48, 699 ± 48, and 429 ± 55 mL H2/g of cat.min, respectively, which is only 282 ± 11 mL H2/g of cat.min for the native g-C3N4-catalyzed one. The activation energies (Ea) were found to be relatively low, such as 31.2, 26.9, and 31.2 kJ/mol, for the reactions catalyzed by B@g-C3N4, P@g-C3N4, and S@g-C3N4, respectively. In addition, in the reuse studies, it was concluded that B@g-C3N4, P@g-C3N4, and S@g-C3N4 catalysts can readily complete the reaction with 100% conversion, even in five consecutive uses, and afforded promising potential with more than 80% activity for each use

The Impact of Innovative Teaching Approaches on Biotechnology Knowledge and Laboratory Experiences of Science Teachers

The current study presents an evaluation of the laboratory instructional tasks prepared based on innovative teaching approaches (research-inquiry, problem solving, project, argumentation and web-based interdisciplinary learning approaches) designed to enhance science teachers’ biotechnology knowledge, awareness and laboratory experiences. The laboratory instructional tasks developed by the researchers aim to improve the laboratory experiences, as well as support the teaching of biotechnology through innovative teaching approaches. For this purpose, in-service training course titled Biotechnology Education Practices was conducted with the voluntary participation of science teachers (n = 17). The current study employed the embedded design. The quantitative part of the embedded design is designed as the single group pretest-posttest model and the qualitative part of it is designed as the case study. The data of the current study were collected through the Biotechnology Awareness Questionnaire, Biotechnology Evaluation Questions, The Laboratory Self-Evaluation form and worksheets. The results obtained from the analyses revealed that the instructional tasks conducted within the context of the Biotechnology Education Practices resulted in significant effects on the science teachers’ biotechnology knowledge and awareness and that the innovative teaching approaches were effective in developing the science teachers’ laboratory experiences. It would be useful to use laboratory instructional tasks enriched with innovative teaching approaches in teaching biotechnology subjects

Description of Oxalicibacterium horti sp. nov. and Oxalicibacterium faecigallinarum sp. nov., new aerobic, yellow-pigmented, oxalotrophic bacteria

Three strains of aerobic, Gram-negative, rod-shaped, non-spore-forming, yellow-pigmented bacteria (OD1T, YOxT and NS13), which were isolated in previous studies by enrichment in a mineral medium with potassium oxalate as the sole carbon source, were characterized. On the basis of 16S rRNA gene sequence similarity, strains OD1T, YOxT and NS13 belong to the Betaproteobacteria, most closely related to Oxalicibacterium flavum TA17T (97.2–99.7% sequence similarity). The major whole-cell fatty acids were C16:0, C16:1ω7c and C17:0 cyclo. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains OD1T and YOxT from O. flavum TA17T and from each other. Therefore, it is concluded that the strains OD1T and YOxT represent novel species within the genus Oxalicibacterium, for which the names Oxalicibacterium horti sp. nov. (type strain OD1T=DSM 21640T=NBRC 13594T) and Oxalicibacterium faecigallinarum sp. nov. (type strain YOxT=DSM 21641T=CCM 2767T) are proposedPeer reviewe

Enhanced Bioactive Properties of Halloysite Nanotubes via Polydopamine Coating

Halloysite nanotubes (HNT) were coated five times with dopamine (DOPA) in a tris buffer medium at pH 8.5 to acquire polydopamine-coated HNTs (PDOPA@HNT), e.g., PDOPA1@HNT, PDOPA3@HNT, and PDOPA5@HNT. Upon coating HNT with PDOPA, the surface area, pore volume, and pore size were decreased depending on the number of coatings. While the surface area of HNT was 57.9 m2/g, by increasing the number of coatings from 1 to 5, it was measured as 55.9, 53.4, 53.3, 47.4, and 46.4 m2/g, respectively. The isoelectric point (IEP) for HNTs was determined as 4.68, whereas these values are estimated as 2.31 for PDOPA1@HNTs, 3.49 for PDOPA3@HNT, and 3.55 for PDOPA5@HNT. Three different antioxidant studies were conducted for HNT and PDOPA@HNT, and the total phenol (TPC) value of HNT was found to be 150.5 ± 45.9 µmol gallic acid (GA) equivalent. The TPC values for PDOPA1@HNT, PDOPA3@HNT and PDOPA5@HNT coatings were found to be 405.5 ± 25.0, 750.0 ± 69.9, and 1348.3 ± 371.7 µmol GA equivalents, respectively. The Fe(II) chelation capacity of HNT was found to be 20.5% ± 1.2%, while the PDOPA1@HNT, PDOPA3@HNT and PDOPA5@HNT values were found to be 49.9 ± 6.5, 36.6 ± 12.7 and 25.4 ± 1.2%, respectively. HNT and PDOPA@HNTs inhibited the α-glucosidase (AG) enzyme to greater extents than acetylcholinesterase (AChE). As a result, the DOPA modification of HNTs was rendered to provide additional characteristics, e.g., antioxidant properties and higher AChE and AG enzymes inhibition capabilities. Therefore, PDOPA@HNTs have great potential as biomaterials