DOCSLIB.ORG

Isolation and Characterization of a Salt-Tolerant Denitrifying Bacterium Alishewanella Sp

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Isolation and Characterization of a Salt-Tolerant Denitrifying Bacterium Alishewanella Sp www.nature.com/scientificreports OPEN Isolation and characterization of a salt-tolerant denitrifying bacterium Alishewanella sp. F2 from seawall muddy water Rui Cheng1,2,3, Xinyi Wang1,3,4, Hui Zhu1,3 ✉ , Baixing Yan1,3, Brian Shutes5, Yingying Xu6, Baorong Fu4 & Huiyang Wen1,3 A salt-tolerant denitrifying bacterium strain F2 was isolated from seawall muddy water in Dalian City, Liaoning Province, China. Strain F2 was identifed by morphological observations, physiological and biochemical characteristics and 16 S rDNA identifcation. The salt tolerance of strain F2 was verifed and – the factors afecting the removal ability of strain F2 to nitrous nitrogen (NO2 N) and nitrate nitrogen – (NO3 N) in saline conditions were investigated. Strain F2 was identifed as Alishewanella sp., named Alishewanella sp. F2. Strain F2 can tolerate NaCl concentrations up to 70 g/L, and its most efcient denitrifcation capacity was observed at NaCl concentrations of 0−30 g/L. In the medium with NaCl – – concentrations of 0−30 g/L, strain F2 exhibited high removal efciencies of NO2 N and NO3 N, with – – the removal percentages for both NO2 N and NO3 N of approximately 99%. In saline conditions with 30 g/L NaCl, the optimum culture pH, NaNO2 initial concentrations and inoculation sizes of strain F2 – were 8−10, 0.4−0.8 g/L and 5−7%, respectively. Strain F2 was highly efective in removing NO2 N and – NO3 N in saline conditions, and it has a good application potential in saline wastewater treatment. In the past 40 years, with the rapid development of aquaculture industry in coastal areas of China, a large amount of coastal aquaculture wastewater has been discharged, which brought about various negative impacts on the environment1. Te coastal aquaculture wastewater usually contains both inorganic salts (on average of 10−30 g/L NaCl) and many contaminants including nitrogen2. Large amounts of nitrogen pollutants (i.e., nitrous nitrogen – – (NO2 N) and nitrate nitrogen (NO3 N)) which are continuously released from the uneaten feed residue can result in the increase of inorganic nitrogen pollution in aquaculture water year by year1,3. Furthermore, with the rapid development of industrialization, a large number of saline wastewater sources, e.g., vegetable pickled wastewater4, textile wastewater5, and oily wastewater6, etc., with NaCl concentrations exceeding 30 g/L have been produced in various industrial processes. Most saline industrial wastewater also contains a large amount of nitrogen pollut- ants7,8. Te increasing discharge of saline wastewater from aquaculture and industry without any treatment has threatened the aquatic, terrestrial and wetland ecosystems9,10. Terefore, the removal of nitrogen pollutants from saline wastewater has become an urgent problem. Nitrite, an intermediate product of nitrifcation and denitrifcation, is frequently detected in water bodies and seriously threatens the aquatic organisms and human health11,12. Te concentration of nitrite in wastewater is up to 50 mg/L or more11. High concentrations of nitrite seriously endanger the growth and normal metabolism of aquatic organisms. Humans accidentally drinking water containing high concentration of nitrite could easily lead to impaired intelligence and form strong carcinogens in the human body (e.g., nitrosamines), and even lead to death. As the most stable form of nitrogenous compounds in the aerobic environment, nitrate has a high solubil- ity and can migrate and difuse rapidly in water, resulting in secondary pollution13,14. Te discharging of untreated 1Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, P R China. 2University of Chinese Academy of Sciences, Beijing, 100049, P R China. 3Jilin Provincial Engineering Center of CWs Design in Cold Region & Beautiful Country Construction, Changchun, 130102, P R China. 4School of Environment, Liaoning University, Shenyang, 110036, P R China. 5Urban Pollution Research Centre, Middlesex University, Hendon, London, NW4 4BT, UK. 6Key Laboratory of Songliao Aquatic Environment, Ministry of Education, Jilin Jianzhu University, Changchun, 130118, P R China. ✉e-mail: [email protected] SCIENTIFIC REPORTS | (2020) 10:10002 | https://doi.org/10.1038/s41598-020-66989-5 1 www.nature.com/scientificreports/ www.nature.com/scientificreports – – – – – – NO2 N initial NO2 N efuent NO2 N removal NO3 N initial NO3 N efuent NO3 N removal Strain concentration(mg/L) concentration(mg/L) percentage(%) concentration(mg/L) concentration(mg/L) percentage(%) F1 115.90 ± 4.63 1.43 ± 0.12 98.76 42.47 ± 1.19 6.43 ± 1.98 84.85 F2 106.87 ± 4.58 1.73 ± 0.54 98.38 45.60 ± 1.77 1.77 ± 0.54 96.13 F3 105.50 ± 3.09 1.37 ± 0.45 98.70 45.00 ± 2.30 4.33 ± 1.89 90.37 – – Table 1. Removal efect of NO2 N and NO3 N by strains in denitrifcation medium afer 5 d cultivation. and unqualifed wastewater containing nitrate into surface water bodies will bring serious potential safety hazards 15 – and threaten the growth of plants, animals and human health . Terefore, efectively reducing the NO2 N and – NO3 N concentrations in water is of great practical signifcance for both ecosystem and human health. Te main technologies for removing nitrogen from wastewater include physical, chemical and biological methods16–19. Compared with physical and chemical methods, biological methods have the advantages of high efciency, low energy consumption, low cost, easy implementation, etc., and have been widely used to remove – – – NO2 N from wastewater. Denitrifcation can convert NO2 N and NO3 N into gaseous nitrogen (i.e., nitrogen (N2) 20 and nitrous oxide (N2O)), and fundamentally solve the nitrogen pollution problem in water . Several nitrite-type denitrifying bacteria, e.g., Acinetobacter baumannii21, Pseudomonas putida22, and Pseudomonas tolaasii23, etc., – have been screened and were proved to be efcient in removing NO2 N from wastewater. However, saline waste- water contains not only high concentrations of nitrogen but also a large amount of soluble salts. Te presence of salts can signifcantly and negatively afect the removal of pollutants by microorganisms24,25. When microorgan- isms are exposed to highly saline environment, osmotic pressure is increased, resulting in the excessive loss of water in general microbial cells, the separation of protoplasm, the inhibition of microbial growth and metabo- lism, and even death26. Te denitrifcation capacity of most denitrifying bacteria is inhibited by high salinity27. – – Terefore, salt-tolerant denitrifying bacteria with efcient NO2 N and NO3 N removal ability are required to be isolated for the treatment of saline wastewater. Te objectives of this study are to: 1) isolate and identify a salt-tolerant denitrifying bacterium strain F2 from seawall muddy water; 2) validate the salt tolerance as well as the denitrifcation capacity of strain F2; and 3) evaluate the efects of initial pH, NaNO2 initial concentration and inoculation size on the denitrifcation capacity of strain F2 in saline conditions. Te results of this study will provide efcient microbial resource and optimal process parameters for microbial denitrifcation of saline wastewater, which is of great signifcance for protecting the water environment safety and human health. Results Isolation of denitrifying bacteria. An anoxic condition was created by submerged culturing of denitrifca- tion medium with NaNO2 as the sole nitrogen source, but a small amount of NaNO2 was still oxidized and rapidly 28 converted into NaNO3 . Afer repeating three times of enrichment and isolation, three strains of denitrifying bacteria with nitrite as sole nitrogen source were obtained, and numbered F1, F2 and F3, respectively. Te three strains became turbid during the enrichment and cultivation in the denitrifcation medium that was accompanied 29 by diferent degrees of gas generation (i.e., N2, N2O and/or nitric oxide (NO)) . Te enrichment cultivation of each strain cultivated for 5 d is shown in Fig. S1 (in supplementary material). – – Table 1 shows the removal percentages of NO2 N and NO3 N by each respective strain. Afer a 5 d cultivation, – the removal percentages of NO2 N in denitrifcation medium by all the three strains were above 98%. However, – the removal percentages of NO3 N by strain F2 were higher than that of other strains. Te removal percentages of – – NO2 N and NO3 N by strain F2 were 98.38% and 96.13%, respectively, and gas was produced concomitantly in a + 5 d cultivation. During the 5 d of cultivation, ammonia nitrogen (NH4 -N) concentration in the medium of strain F2 increased slightly, and the total nitrogen (TN) removal percentage by strain F2 was 20.99% (Fig. S2 in supple- – – mentary material), which indicated that some of the NO2 N and NO3 N in the medium were transformed into + NH4 -N, and some were transformed into nitrogen-containing substances which are necessary for the growth of strain F2 through assimilation. Besides, according to the conservation of elements, the removal of TN in the medium was mainly due to the emission of gaseous nitrogen (i.e., N2, N2O and/or NO). Afer comprehensive analysis, strain F2, an ideal bacterium, was selected as the research object in the subsequent experiments. Identifcation of strain F2. Te physiological and biochemical characteristics of strain F2 are shown in Table 2. Te extracted bacterial DNA was amplifed using 16 S rDNA primers to a 1033 bp amplifed fragment (Fig. S3 in supplementary material). Te phylogenetic tree constructed by the MEGA 4.0 version sofware is shown in Fig. 1. Te 16 S rDNA identifcation reveals that strain F2 was 99.81% homology genetic related with Alishewanella sp. N5 (GenBank accession no. EU287929.1). Terefore, according to the morphological obser- vation and 16 S rDNA gene analysis, strain F2 was identifed as Alishewanella sp., named Alishewanella sp. F2 (GenBank accession no. MN396708). It was deposited at the China General Microbiological Culture Collection Center (CGMCC) on March 25, 2019, numbered CGMCC No: 17433.
Load more

Recommended publications
  • Characterization of a Microbial Community Capable of Nitrification At
    Bioresource Technology 101 (2010) 491–500 Contents lists available at ScienceDirect Bioresource Technology journal homepage: www.elsevier.com/locate/biortech Characterization of a microbial community capable of nitrification at cold temperature Thomas F. Ducey *, Matias B. Vanotti, Anthony D. Shriner, Ariel A. Szogi, Aprel Q. Ellison Coastal Plains Soil, Water, and Plant Research Center, Agricultural Research Service, USDA, 2611 West Lucas Street, Florence, SC 29501, United States article info abstract Article history: While the oxidation of ammonia is an integral component of advanced aerobic livestock wastewater Received 5 February 2009 treatment, the rate of nitrification by ammonia-oxidizing bacteria is drastically reduced at colder temper- Received in revised form 30 July 2009 atures. In this study we report an acclimated lagoon nitrifying sludge that is capable of high rates of nitri- Accepted 30 July 2009 fication at temperatures from 5 °C (11.2 mg N/g MLVSS/h) to 20 °C (40.4 mg N/g MLVSS/h). The Available online 5 September 2009 composition of the microbial community present in the nitrifying sludge was investigated by partial 16S rRNA gene sequencing. After DNA extraction and the creation of a plasmid library, 153 partial length Keywords: 16S rRNA gene clones were sequenced and analyzed phylogenetically. Over 80% of these clones were Nitrite affiliated with the Proteobacteria, and grouped with the b- (114 clones), - (7 clones), and -classes (2 Ammonia-oxidizing bacteria c a Nitrosomonas clones). The remaining clones were affiliated with the Acidobacteria (1 clone), Actinobacteria (8 clones), Activated sludge Bacteroidetes (16 clones), and Verrucomicrobia (5 clones). The majority of the clones belonged to the genus 16S rRNA gene Nitrosomonas, while other clones affiliated with microorganisms previously identified as having floc forming or psychrotolerance characteristics.
    [Show full text]
  • Alishewanella Jeotgali Sp. Nov., Isolated from Traditional Fermented Food, and Emended Description of the Genus Alishewanella
    International Journal of Systematic and Evolutionary Microbiology (2009), 59, 2313–2316 DOI 10.1099/ijs.0.007260-0 Alishewanella jeotgali sp. nov., isolated from traditional fermented food, and emended description of the genus Alishewanella Min-Soo Kim,1,2 Seong Woon Roh,1,2 Young-Do Nam,1,2 Ho-Won Chang,1 Kyoung-Ho Kim,1 Mi-Ja Jung,1 Jung-Hye Choi,1 Eun-Jin Park1 and Jin-Woo Bae1,2 Correspondence 1Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee Jin-Woo Bae University, Seoul 130-701, Republic of Korea [email protected] 2University of Science and Technology, Biological Resources Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea A novel Gram-negative and facultative anaerobic strain, designated MS1T, was isolated from gajami sikhae, a traditional fermented food in Korea made from flatfish. Strain MS1T was motile, rod-shaped and oxidase- and catalase-positive, and required 1–2 % (w/v) NaCl for growth. Growth occurred at temperatures ranging from 4 to 40 6C and the pH range for optimal growth was pH 6.5–9.0. Strain MS1T was capable of reducing trimethylamine oxide, nitrate and thiosulfate. Phylogenetic analysis placed strain MS1T within the genus Alishewanella. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MS1T was related closely to Alishewanella aestuarii B11T (98.67 % similarity) and Alishewanella fetalis CCUG 30811T (98.04 % similarity). However, DNA–DNA reassociation experiments between strain MS1T and reference strains showed relatedness values ,70 % (42.6 and 14.8 % with A.
    [Show full text]
  • Microbial Diversity of Drilling Fluids from 3000 M Deep Koyna Pilot
    Science Reports Sci. Dril., 27, 1–23, 2020 https://doi.org/10.5194/sd-27-1-2020 © Author(s) 2020. This work is distributed under the Creative Commons Attribution 4.0 License. Microbial diversity of drilling fluids from 3000 m deep Koyna pilot borehole provides insights into the deep biosphere of continental earth crust Himadri Bose1, Avishek Dutta1, Ajoy Roy2, Abhishek Gupta1, Sourav Mukhopadhyay1, Balaram Mohapatra1, Jayeeta Sarkar1, Sukanta Roy3, Sufia K. Kazy2, and Pinaki Sar1 1Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India 2Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, 713209, West Bengal, India 3Ministry of Earth Sciences, Borehole Geophysics Research Laboratory, Karad, 415114, Maharashtra, India Correspondence: Pinaki Sar ([email protected], [email protected]) Received: 24 June 2019 – Revised: 25 September 2019 – Accepted: 16 December 2019 – Published: 27 May 2020 Abstract. Scientific deep drilling of the Koyna pilot borehole into the continental crust up to a depth of 3000 m below the surface at the Deccan Traps, India, provided a unique opportunity to explore microbial life within the deep granitic bedrock of the Archaean Eon. Microbial communities of the returned drilling fluid (fluid re- turned to the mud tank from the underground during the drilling operation; designated here as DF) sampled during the drilling operation of the Koyna pilot borehole at a depth range of 1681–2908 metres below the surface (m b.s.) were explored to gain a glimpse of the deep biosphere underneath the continental crust. Change of pH 2− to alkalinity, reduced abundance of Si and Al, but enrichment of Fe, Ca and SO4 in the samples from deeper horizons suggested a gradual infusion of elements or ions from the crystalline bedrock, leading to an observed geochemical shift in the DF.
    [Show full text]
  • Genomes Outside SIGS October - November 2012 Burkholderia Thailandensis MSMB43, Sequence Hydrogenophaga Sp
    Standards in Genomic Sciences (2012) 7:331-350 DOI:10.4056/sigs.3597227 Genome sequences published outside of Standards in Genomic Sciences, October - November 2012 Oranmiyan W. Nelson1 and George M. Garrity1 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the biblio- graphic data for such references to the SIGS editorial office. Domain Archaea Alcaligenes faecalis subsp. faecalis NCIB 8687, Phylum Crenarchaeota sequence accession AKMR01000001 through “Thermogladius cellulolyticus” 1633, AKMR01000186 [9] sequence accession CP003531 [1] Alishewanella aestuarii Strain B11T, sequence accession ALAB00000000 [10] Phylum Euryarchaeota Methanomassiliicoccus luminyensis, se- Alishewanella agri BL06T, sequence accession quence accession CAJE01000001 AKKU00000000 [11] through CAJE01000026 [2] Bartonella birtlesii strain IBS 135T, sequence Pyrococcus sp. Strain ST04, sequence accession AKIP00000000 [12] accession CP003534 [3] Brucella abortus A13334, sequence accession CP003176.1 (Chromosome I), CP003177.1 Domain Bacteria (Chromosome II) [13] Nitrospirae Phylum Brucella canis Strain HSK A52141, sequence Leptospirillum ferrooxidans Strain C2- accession CP003174.1 (chromosome I), and 3, sequence accession AP012342 [4] CP003175.1 (chromosome II) [14] Phylum Cyanobacteria Brucella melitensis 16M13w, sequence acces- Prochlorococcus marinus MED4, se- sion AHWE00000000 [15] quence accession BX548174 [5] Brucella melitensis 16M1w, sequence acces- sion AHWD00000000 [15] Phylum Proteobacteria Acinetobacter sp.
    [Show full text]
  • Alishewanella Aestuarii Sp. Nov., Isolated from Tidal Flat Sediment, and Emended Description of the Genus Alishewanella
    International Journal of Systematic and Evolutionary Microbiology (2009), 59, 421–424 DOI 10.1099/ijs.0.65643-0 Alishewanella aestuarii sp. nov., isolated from tidal flat sediment, and emended description of the genus Alishewanella Seong Woon Roh,1,2 Young-Do Nam,1,2 Ho-Won Chang,2 Kyoung-Ho Kim,2 Min-Soo Kim,1,2 Hee-Mock Oh2 and Jin-Woo Bae1,2,3 Correspondence 1University of Science & Technology, 52, Eoeun-dong, Daejeon 305-333, Republic of Korea Jin-Woo Bae 2Biological Resource Center, KRIBB, Daejeon 305-806, Republic of Korea [email protected] 3Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea A Gram-negative strain, B11T, was isolated from tidal flat sediment in Yeosu, Republic of Korea. Strain B11T did not require NaCl for growth and grew between 18 and 44 6C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B11T was associated with the genus Alishewanella and was closely related to the type strain of Alishewanella fetalis (98.3 % similarity). Within the phylogenetic tree, the novel isolate shared a branching point with A. fetalis. Analysis of 16S rRNA gene sequences and DNA–DNA relatedness, as well as physiological and biochemical tests, indicated genotypic and phenotypic differences between strain B11T and the type strain of A. fetalis. Thus, strain B11T is proposed as a representative of a novel species, Alishewanella aestuarii sp. nov.; the type strain is B11T (5KCTC 22051T 5DSM 19476T). The genus Alishewanella, proposed by Fonnesbech Vogel et description; Table 1 shows a comparison between the al.
    [Show full text]
  • Draft Genomic Sequence of a Chromate- and Sulfate-Reducing
    Xia et al. Standards in Genomic Sciences (2016) 11:48 DOI 10.1186/s40793-016-0169-3 SHORT GENOME REPORT Open Access Draft genomic sequence of a chromate- and sulfate-reducing Alishewanella strain with the ability to bioremediate Cr and Cd contamination Xian Xia1, Jiahong Li1, Shuijiao Liao1,2, Gaoting Zhou1,2, Hui Wang1, Liqiong Li1, Biao Xu1 and Gejiao Wang1* Abstract Alishewanella sp. WH16-1 (= CCTCC M201507) is a facultative anaerobic, motile, Gram-negative, rod-shaped bacterium isolated from soil of a copper and iron mine. This strain efficiently reduces chromate (Cr6+) to the much 3+ 2− 2− 2− 2+ less toxic Cr . In addition, it reduces sulfate (SO4 )toS . The S could react with Cd to generate precipitated CdS. Thus, strain WH16-1 shows a great potential to bioremediate Cr and Cd contaimination. Here we describe the features of this organism, together with the draft genome and comparative genomic results among strain WH16-1 and other Alishewanella strains. The genome comprises 3,488,867 bp, 50.4 % G + C content, 3,132 protein-coding genes and 80 RNA genes. Both putative chromate- and sulfate-reducing genes are identified. Keywords: Alishewanella, Chromate-reducing bacterium, Sulfate-reducing bacterium, Cadmium, Chromium Abbreviation: PGAP, Prokaryotic Genome Annotation Pipeline Introduction Alishewanella sp. WH16-1 was isolated from mining The genus Alishewanella was established by Vogel et al., soil in 2009. This strain could resist to multiple heavy in 2000 with Alishewanella fetalis as the type species. It metals. During cultivation, it could efficiently reduce the belongs to the family Alteromonadaceae of the class toxic chromate (Cr6+) to the much less toxic and less 3+ 2− Gammaproteobacteria [1].
    [Show full text]
  • Cultivation-Based Quantification and Identification of Bacteria at Two
    microorganisms Communication Cultivation-Based Quantification and Identification of Bacteria at Two Hygienic Key Sides of Domestic Washing Machines Susanne Jacksch 1,2 , Huzefa Zohra 1, Mirko Weide 3, Sylvia Schnell 2 and Markus Egert 1,* 1 Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, 78054 Villingen-Schwenningen, Germany; [email protected] (S.J.); [email protected] (H.Z.) 2 Research Centre for BioSystems, Land Use, and Nutrition (IFZ), Institute of Applied Microbiology, Justus-Liebig-University Giessen, 35392 Giessen, Germany; [email protected] 3 International Research & Development–Laundry & Home Care, Henkel AG & Co. KGaA, 40191 Düsseldorf, Germany; [email protected] * Correspondence: [email protected]; Tel.: +49-(7720)-307-4554; Fax: +49-(7720)-307-4207 Abstract: Detergent drawer and door seal represent important sites for microbial life in domes- tic washing machines. Interestingly, quantitative data on the microbial contamination of these sites is scarce. Here, 10 domestic washing machines were swab-sampled for subsequent bacte- rial cultivation at four different sampling sites: detergent drawer and detergent drawer chamber, as well as the top and bottom part of the rubber door seal. The average bacterial load over all washing machines and sites was 2.1 ± 1.0 × 104 CFU cm−2 (average number of colony forming units ± standard error of the mean (SEM)). The top part of the door seal showed the lowest contami- 1 −2 nation (11.1 ± 9.2 × 10 CFU cm ), probably due to less humidity. Out of 212 isolates, 178 (84%) were identified on the genus level, and 118 (56%) on the species level using matrix-assisted laser Citation: Jacksch, S.; Zohra, H.; desorption/ionization (MALDI) Biotyping, resulting in 29 genera and 40 identified species across all Weide, M.; Schnell, S.; Egert, M.
    [Show full text]
  • Phylogenomic and Comparative Analysis of the Distribution And
    www.nature.com/scientificreports OPEN Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP Received: 25 August 2017 Accepted: 20 March 2018 riboswitches in fungi Published: xx xx xxxx Sumit Mukherjee1, Matan Drory Retwitzer2, Danny Barash2 & Supratim Sengupta 1 Riboswitches are metabolite or ion sensing cis-regulatory elements that regulate the expression of the associated genes involved in biosynthesis or transport of the corresponding metabolite. Among the nearly 40 diferent classes of riboswitches discovered in bacteria so far, only the TPP riboswitch has also been found in algae, plants, and in fungi where their presence has been experimentally validated in a few instances. We analyzed all the available complete fungal and related genomes and identifed TPP riboswitch-based regulation systems in 138 fungi and 15 oomycetes. We fnd that TPP riboswitches are most abundant in Ascomycota and Basidiomycota where they regulate TPP biosynthesis and/ or transporter genes. Many of these transporter genes were found to contain conserved domains consistent with nucleoside, urea and amino acid transporter gene families. The genomic location of TPP riboswitches when correlated with the intron structure of the regulated genes enabled prediction of the precise regulation mechanism employed by each riboswitch. Our comprehensive analysis of TPP riboswitches in fungi provides insights about the phylogenomic distribution, regulatory patterns and functioning mechanisms of TPP riboswitches across diverse fungal species and provides a useful resource that will enhance the understanding of RNA-based gene regulation in eukaryotes. Riboswitches are conserved non-coding structural RNA sensors that bind specifc metabolites and regulate gene expression1–4. A riboswitch is mainly composed of two domains; a highly conserved aptamer domain, which is responsible for binding of metabolites, and the expression platform that changes conformation on metabolite binding and regulates the expression of associated genes2.
    [Show full text]
  • Taxonomic Hierarchy of the Phylum Proteobacteria and Korean Indigenous Novel Proteobacteria Species
    Journal of Species Research 8(2):197-214, 2019 Taxonomic hierarchy of the phylum Proteobacteria and Korean indigenous novel Proteobacteria species Chi Nam Seong1,*, Mi Sun Kim1, Joo Won Kang1 and Hee-Moon Park2 1Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea 2Department of Microbiology & Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea *Correspondent: [email protected] The taxonomic hierarchy of the phylum Proteobacteria was assessed, after which the isolation and classification state of Proteobacteria species with valid names for Korean indigenous isolates were studied. The hierarchical taxonomic system of the phylum Proteobacteria began in 1809 when the genus Polyangium was first reported and has been generally adopted from 2001 based on the road map of Bergey’s Manual of Systematic Bacteriology. Until February 2018, the phylum Proteobacteria consisted of eight classes, 44 orders, 120 families, and more than 1,000 genera. Proteobacteria species isolated from various environments in Korea have been reported since 1999, and 644 species have been approved as of February 2018. In this study, all novel Proteobacteria species from Korean environments were affiliated with four classes, 25 orders, 65 families, and 261 genera. A total of 304 species belonged to the class Alphaproteobacteria, 257 species to the class Gammaproteobacteria, 82 species to the class Betaproteobacteria, and one species to the class Epsilonproteobacteria. The predominant orders were Rhodobacterales, Sphingomonadales, Burkholderiales, Lysobacterales and Alteromonadales. The most diverse and greatest number of novel Proteobacteria species were isolated from marine environments. Proteobacteria species were isolated from the whole territory of Korea, with especially large numbers from the regions of Chungnam/Daejeon, Gyeonggi/Seoul/Incheon, and Jeonnam/Gwangju.
    [Show full text]
  • TPP Riboswitch Characterization in Alishewanella Tabrizica And
    Erschienen in: Microbiological Research ; 195 (2017). - S. 71-80 https://dx.doi.org/10.1016/j.micres.2016.11.003 TPP riboswitch characterization in Alishewanella tabrizica and Alishewanella aestuarii and comparison with other TPP riboswitches a,b,c d a e,f Elnaz Mehdizadeh Aghdam , Malte Sinn , Vahideh Tarhriz , Abolfazl Barzegar , d,∗∗ a,b,∗ Jörg S. Hartig , Mohammad Saeid Hejazi a Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran b Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran c Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran d Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany e Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran f The School of Advanced Biomedical Sciences (SABS), Tabriz University of Medical Sciences, Tabriz, Iran a b s t r a c t Riboswitches are located in non-coding areas of mRNAs and act as sensors of cellular small molecules, regulating gene expression in response to ligand binding. The TPP riboswitch is the most widespread riboswitch occurring in all three domains of life. However, it has been rarely characterized in environ- mental bacteria other than Escherichia coli and Bacillus subtilis. In this study, TPP riboswitches located in the 5 UTR of thiC operon from Alishewanella tabrizica and Alishewanella aestuarii were identified and characterized. Moreover, affinity analysis of TPP binding to the TPP aptamer domains originated from A. tabrizica, A. aestuarii, E.coli, and B. subtilis were studied and compared using In-line probing and Sur- face Plasmon Resonance (SPR).
    [Show full text]
  • Appendix 1. New and Emended Taxa Described Since Publication of Volume One, Second Edition of the Systematics
    188 THE REVISED ROAD MAP TO THE MANUAL Appendix 1. New and emended taxa described since publication of Volume One, Second Edition of the Systematics Acrocarpospora corrugata (Williams and Sharples 1976) Tamura et Basonyms and synonyms1 al. 2000a, 1170VP Bacillus thermodenitrificans (ex Klaushofer and Hollaus 1970) Man- Actinocorallia aurantiaca (Lavrova and Preobrazhenskaya 1975) achini et al. 2000, 1336VP Zhang et al. 2001, 381VP Blastomonas ursincola (Yurkov et al. 1997) Hiraishi et al. 2000a, VP 1117VP Actinocorallia glomerata (Itoh et al. 1996) Zhang et al. 2001, 381 Actinocorallia libanotica (Meyer 1981) Zhang et al. 2001, 381VP Cellulophaga uliginosa (ZoBell and Upham 1944) Bowman 2000, VP 1867VP Actinocorallia longicatena (Itoh et al. 1996) Zhang et al. 2001, 381 Dehalospirillum Scholz-Muramatsu et al. 2002, 1915VP (Effective Actinomadura viridilutea (Agre and Guzeva 1975) Zhang et al. VP publication: Scholz-Muramatsu et al., 1995) 2001, 381 Dehalospirillum multivorans Scholz-Muramatsu et al. 2002, 1915VP Agreia pratensis (Behrendt et al. 2002) Schumann et al. 2003, VP (Effective publication: Scholz-Muramatsu et al., 1995) 2043 Desulfotomaculum auripigmentum Newman et al. 2000, 1415VP (Ef- Alcanivorax jadensis (Bruns and Berthe-Corti 1999) Ferna´ndez- VP fective publication: Newman et al., 1997) Martı´nez et al. 2003, 337 Enterococcus porcinusVP Teixeira et al. 2001 pro synon. Enterococcus Alistipes putredinis (Weinberg et al. 1937) Rautio et al. 2003b, VP villorum Vancanneyt et al. 2001b, 1742VP De Graef et al., 2003 1701 (Effective publication: Rautio et al., 2003a) Hongia koreensis Lee et al. 2000d, 197VP Anaerococcus hydrogenalis (Ezaki et al. 1990) Ezaki et al. 2001, VP Mycobacterium bovis subsp. caprae (Aranaz et al.
    [Show full text]
  • Isolation and Characterization of ISA Degrading Alkaliphilic Bacteria
    Isolation and Characterization of ISA Degrading Alkaliphilic Bacteria Zohier Salah (Researcher) A thesis submitted to the University of Huddersfield in the partial fulfilment of the requirements for the degree of Doctor of Philosophy School of Applied Science December 2017 Acknowledgment Praise be to Allah through whose mercy (and favors) all good things are accomplished Firstly, I would like to express my sincere gratitude to my main supervisor Professor Paul N. Humphreys who gave me the opportunity to work with him and for the continuous support of my PhD study and related research, for his patience, motivation, and immense knowledge. His guidance helped me in all the time of research and writing of this thesis. Also, I wish to express my appreciation to my second supervisor, Professor Andy Laws for all the assistance he offered. Without they precious support it would not be possible to conduct this research. Special thanks go to the Government of Libya for providing me with the financial support for this study. I would also like to thank all the laboratory support staff in the School of Applied Sciences, University of Huddersfield, for all the support. Sincerely appreciations also go to my family especially, my parents and my virtuous wife Zainab, my son Mohamed and the extended my family, especially my brother Mr. Ahmed Salah. Finally, but by no means least, thanks to all my colleagues in the research group who helped with experience, ideas and discussions during my studies, Dr Simon P Rout, Dr Isaac A Kyeremeh, Dr Christopher J Charles and to all who contributed in diverse ways to make my research at the University of Huddersfield a success.
    [Show full text]