To Obtain a Determination of Whether an Organism Is a New Organism
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Acetobacter Sacchari Sp. Nov., for a Plant Growth-Promoting Acetic Acid Bacterium Isolated in Vietnam
Annals of Microbiology (2019) 69:1155–11631163 https://doi.org/10.1007/s13213-019-01497-0 ORIGINAL ARTICLE Acetobacter sacchari sp. nov., for a plant growth-promoting acetic acid bacterium isolated in Vietnam Huong Thi Lan Vu1,2 & Pattaraporn Yukphan3 & Van Thi Thu Bui1 & Piyanat Charoenyingcharoen3 & Sukunphat Malimas4 & Linh Khanh Nguyen1 & Yuki Muramatsu5 & Naoto Tanaka6 & Somboon Tanasupawat7 & Binh Thanh Le2 & Yasuyoshi Nakagawa5 & Yuzo Yamada3,8,9 Received: 21 January 2019 /Accepted: 7 July 2019 /Published online: 18 July 2019 # Università degli studi di Milano 2019 Abstract Purpose Two bacterial strains, designated as isolates VTH-Ai14T and VTH-Ai15, that have plant growth-promoting ability were isolated during the study on acetic acid bacteria diversity in Vietnam. The phylogenetic analysis based on 16S rRNA gene sequences showed that the two isolates were located closely to Acetobacter nitrogenifigens RG1T but formed an independent cluster. Methods The phylogenetic analysis based on 16S rRNA gene and three housekeeping genes’ (dnaK, groEL, and rpoB) sequences were analyzed. The genomic DNA of the two isolates, VTH-Ai14T and VTH-Ai15, Acetobacter nitrogenifigens RG1T, the closest phylogenetic species, and Acetobacter aceti NBRC 14818T were hybridized and calculated the %similarity. Then, phenotypic and chemotaxonomic characteristics were determined for species’ description using the conventional method. Results The 16S rRNA gene and concatenated of the three housekeeping genes phylogenetic analysis suggests that the two isolates were constituted in a species separated from Acetobacter nitrogenifigens, Acetobacter aceti,andAcetobacter sicerae. The two isolates VTH-Ai14T and VTH-Ai15 showed 99.65% and 98.65% similarity of 16S rRNA gene when compared with Acetobacter nitrogenifigens and Acetobacter aceti and they were so different from Acetobacter nitrogenifigens RG1T with 56.99 ± 3.6 and 68.15 ± 1.8% in DNA-DNA hybridization, when isolates VTH-Ai14T and VTH-Ai15 were respectively labeled. -
Inhibition of MRN Activity by a Telomere Protein Motif
ARTICLE https://doi.org/10.1038/s41467-021-24047-2 OPEN Inhibition of MRN activity by a telomere protein motif Freddy Khayat1,6, Elda Cannavo2,6, Majedh Alshmery1, William R. Foster1, Charly Chahwan 1,4, Martino Maddalena1,5, Christopher Smith 1, Antony W. Oliver 1, Adam T. Watson1, Antony M. Carr 1, ✉ Petr Cejka2,3 & Alessandro Bianchi 1 The MRN complex (MRX in Saccharomyces cerevisiae, made of Mre11, Rad50 and Nbs1/Xrs2) 1234567890():,; initiates double-stranded DNA break repair and activates the Tel1/ATM kinase in the DNA damage response. Telomeres counter both outcomes at chromosome ends, partly by keeping MRN-ATM in check. We show that MRX is disabled by telomeric protein Rif2 through an N- terminal motif (MIN, MRN/X-inhibitory motif). MIN executes suppression of Tel1, DNA end- resection and non-homologous end joining by binding the Rad50 N-terminal region. Our data suggest that MIN promotes a transition within MRX that is not conductive for endonuclease activity, DNA-end tethering or Tel1 kinase activation, highlighting an Achilles’ heel in MRN, which we propose is also exploited by the RIF2 paralog ORC4 (Origin Recognition Complex 4) in Kluyveromyces lactis and the Schizosaccharomyces pombe telomeric factor Taz1, which is evolutionarily unrelated to Orc4/Rif2. This raises the possibility that analogous mechanisms might be deployed in other eukaryotes as well. 1 Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK. 2 Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Universitàdella Svizzera italiana (USI), Bellinzona, Switzerland. 3 Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland. -
REPORT on APPLES – Fruit Pathway and Alert List
EU project number 613678 Strategies to develop effective, innovative and practical approaches to protect major European fruit crops from pests and pathogens Work package 1. Pathways of introduction of fruit pests and pathogens Deliverable 1.3. PART 5 - REPORT on APPLES – Fruit pathway and Alert List Partners involved: EPPO (Grousset F, Petter F, Suffert M) and JKI (Steffen K, Wilstermann A, Schrader G). This document should be cited as ‘Wistermann A, Steffen K, Grousset F, Petter F, Schrader G, Suffert M (2016) DROPSA Deliverable 1.3 Report for Apples – Fruit pathway and Alert List’. An Excel file containing supporting information is available at https://upload.eppo.int/download/107o25ccc1b2c DROPSA is funded by the European Union’s Seventh Framework Programme for research, technological development and demonstration (grant agreement no. 613678). www.dropsaproject.eu [email protected] DROPSA DELIVERABLE REPORT on Apples – Fruit pathway and Alert List 1. Introduction ................................................................................................................................................... 3 1.1 Background on apple .................................................................................................................................... 3 1.2 Data on production and trade of apple fruit ................................................................................................... 3 1.3 Pathway ‘apple fruit’ ..................................................................................................................................... -
Signatures of Optimal Codon Usage Predict Metabolic Ecology in Budding Yeasts
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.22.214635; this version posted July 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Signatures of optimal codon usage predict metabolic ecology in budding yeasts 2 Abigail Leavitt LaBella 3 Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA 4 ORCID: 0000-0003-0068-6703 5 [email protected] 6 7 Dana A. Opulente 8 Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy 9 Institute, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, 10 University of Wisconsin-Madison, Madison, WI 53726, USA 11 12 Jacob Steenwyk 13 Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA 14 ORCID: 0000-0002-8436-595X 15 [email protected] 16 17 Chris Todd Hittinger 18 Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy 19 Institute, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, 20 University of Wisconsin-Madison, Madison, WI 53726, USA 21 ORCID: 0000-0001-5088-7461 22 [email protected] 23 24 Antonis Rokas 25 Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA 26 ORCID: 0000-0002-7248-6551 27 [email protected] 28 Running head: Codon usage as a lens into the metabolic ecology of budding yeasts 29 Keywords: Codon usage bias; Budding yeasts; Secondary metabolism; Reverse Ecology bioRxiv preprint doi: https://doi.org/10.1101/2020.07.22.214635; this version posted July 24, 2020. -
An Investigation of Simultaneous Pineapple Vinegar Fermentation Interaction Between Acetic Acid Bacteria and Yeast
As. J. Food Ag-Ind. 2010, 3(01), 192-203 Asian Journal of Food and Agro-Industry ISSN 1906-3040 Available online at www.ajofai.info Research Article An investigation of simultaneous pineapple vinegar fermentation interaction between acetic acid bacteria and yeast Warawut Krusong* and Assanee Vichitraka Faculty of Agro-Industry, King Mongkut’s Institute of Technology Ladkrabang, Chalongkrung Rd., Ladkrabang, Bangkok 10520, Thailand. Author to whom correspondence should be addressed, email: [email protected] This paper was originally presented at Food Innovation Asia, Bangkok, Thailand, August, 2009. Abstract Simultaneous pineapple vinegar fermentation interaction between two microorganisms was investigated, wherein the interaction between acetic acid bacteria (AAB) Acetobacter aceti WK and a flocculate yeast Saccharomyces cerevisiae M30 was conducted. The inoculated yeast was allowed to ferment for 1 - 4 days prior to inoculating the AAB into the fermenting mash. Non-aerated conditions for alcohol fermentation were used to enhance the ability of S. cerevisiae M30, whereas aeration was supplied to assist vinegar fermentation by A. aceti WK. During aeration, alcohol production by S. cerevisiae M30 was drastically decreased and observed, while A. aceti WK cells increased for two more log cycles within 10 days and produced 1.6 – 2.1% acetic acid. By this simultaneous fermentation, the commensalisms interaction was primarily observed by supplying of alcohol to AAB by yeast, while the AAB provided nothing to yeast. The accumulating acetic acid produced by A. aceti WK caused an antagonistic effect on growth of S. cerevisiae M30. Keywords: Acetobacter aceti, Saccharomyces cerevisiae M30, simultaneous pineapple vinegar fermentation, biological interaction, acetic acid bacteria, yeast, commensalisms, antagonistic effect, Thailand. -
Exemption for Acetobacter Aceti
FINAL DECISION DOCUMENT: TSCA SECTION 5(H)(4) EXEMPTION FOR ACETOBACTER ACETI I. BACKGROUND In the September 1, 1994, Federal Register (59 FR 45526), the Environmental Protection Agency (EPA) proposed at 40 CFR Part 700 under section 5(h)(4) of the Toxic Substances Control Act (TSCA), Tier I and Tier II exemptions. These exemptions, which would be found at § 725.400, are exemptions from EPA review and expedited EPA review, respectively, for certain microorganisms under certain use conditions. EPA proposed to include Acetobacter aceti at § 725.420 as a candidate recipient microorganism for the tiered exemptions. Acetobacter aceti is a benign microorganism that is ubiquitous in the environment existing in ecological niches such as flowers, fruits, honey bees, as well as in water and soil. It has a long history of safe use in the fermentation industry for the production of acetic acid from alcohol. This final decision document describes the basis for EPA's decision to include Acetobacter aceti as a recipient microorganism at § 725.420. II. CONDITIONS OF EXEMPTION EPA recognizes that some microorganisms present a low risk when used under specific conditions at general commercial use. Therefore, EPA proposed to institute expedited regulatory processes for certain microorganisms under these specific conditions at the general commercial use stage. Microorganism uses that are exempt would meet criteria addressing: (1) performance based standards for minimizing the numbers of microorganisms emitted from the manufacturing facility; (2) the introduced genetic material; and (3) the recipient microorganism. Microorganisms that qualify for these exemptions, termed Tier I and Tier II, must meet a standard of no unreasonable risk in the exempted use. -
Acetic Acid Bacteria – Perspectives of Application in Biotechnology – a Review
POLISH JOURNAL OF FOOD AND NUTRITION SCIENCES www.pan.olsztyn.pl/journal/ Pol. J. Food Nutr. Sci. e-mail: [email protected] 2009, Vol. 59, No. 1, pp. 17-23 ACETIC ACID BACTERIA – PERSPECTIVES OF APPLICATION IN BIOTECHNOLOGY – A REVIEW Lidia Stasiak, Stanisław Błażejak Department of Food Biotechnology and Microbiology, Warsaw University of Life Science, Warsaw, Poland Key words: acetic acid bacteria, Gluconacetobacter xylinus, glycerol, dihydroxyacetone, biotransformation The most commonly recognized and utilized characteristics of acetic acid bacteria is their capacity for oxidizing ethanol to acetic acid. Those microorganisms are a source of other valuable compounds, including among others cellulose, gluconic acid and dihydroxyacetone. A number of inves- tigations have recently been conducted into the optimization of the process of glycerol biotransformation into dihydroxyacetone (DHA) with the use of acetic acid bacteria of the species Gluconobacter and Acetobacter. DHA is observed to be increasingly employed in dermatology, medicine and cosmetics. The manuscript addresses pathways of synthesis of that compound and an overview of methods that enable increasing the effectiveness of glycerol transformation into dihydroxyacetone. INTRODUCTION glucose to acetic acid [Yamada & Yukphan, 2007]. Another genus, Acetomonas, was described in the year 1954. In turn, Multiple species of acetic acid bacteria are capable of in- in the year 1984, Acetobacter was divided into two sub-genera: complete oxidation of carbohydrates and alcohols to alde- Acetobacter and Gluconoacetobacter, yet the year 1998 brought hydes, ketones and organic acids [Matsushita et al., 2003; another change in the taxonomy and Gluconacetobacter was Deppenmeier et al., 2002]. Oxidation products are secreted recognized as a separate genus [Yamada & Yukphan, 2007]. -
EFFICIENT CULTIVATION of Kluyveromyces Lactis in HIGH CELL DENSITY CULTURE in FED-BATCH CULTIVATION SYSTEM
EFFICIENT CULTIVATION OF Kluyveromyces lactis IN HIGH CELL DENSITY CULTURE IN FED-BATCH CULTIVATION SYSTEM MOHD SHAFIQ B MOHD SUEB A dissertation submitted in fulfillment of the requirements for the award of degree of Master of Engineering (Bioprocess) Faculty of Chemical Engineering Universiti Teknologi Malaysia JUN 2012 PERPUSTAKAN UNIVERSITi MALAYSIA PAHANG 0. Perolef-jan No. Panggilan 4 .' 2uu- o'z ABSTRACT Kluyveromyces lactis is beneficial and well-known yeast due to its status of GRAS that has made the yeast as a vital microorganism for the subject of studies and also the applications of industry such as a possible source of single-cell protein with expected probiotic properties, oligonuci eotide-derived flavour enhancers and lactic acid. In addition, High Cell Density Cultivation (HCDC) of K. lactis has been scientifically and biotechnologically important trend in improving microbial mass and product formation substantially. More importantly, fed-batch strategy has been identified as another effective mean to increase the yield by preventing substrate limitation or inhibition through maintaining medium substrate concentration at a low level during cultivation. In this study, there were two system cultivations have been employed which was batch cultivation and fed-batch cultivation. Further studies have been done under batch cultivation on the aeration effect and dissolved 02, DO. The results showed that 1.0 v/v/inin aeration rate gave relatively high cell dry weight, CDW, 18.6 gIL. On the contrary, the results from DO stat value of 60% showed substantial increment with CDW of 28.7 gIL. As for the fed-batch study, constant feeding rate strategy has been applied with two different feeding substrates i.e complete media and mono-lactate. -
Microbiology of Vinegar: from Isolation, Phenetic Characterization and Detection of Acetic Acid Bacteria to Microbial Profiling of an Industrial Production
Microbiology of Vinegar: from Isolation, Phenetic Characterization and Detection of Acetic Acid Bacteria to Microbial Profiling of an Industrial Production João Nuno Serôdio de Melo Thesis to obtain the Master of Science Degree in Microbiology Supervisor(s): Prof. Rogério Paulo de Andrade Tenreiro Prof. Nuno Gonçalo Pereira Mira Examination Committee: Chairperson: Prof. Jorge Humberto Gomes Leitão Supervisor: Prof. Rogério Paulo de Andrade Tenreiro Member of the Committee: Prof. Rodrigo da Silva Costa December, 2016 Acknowledgements I would like to express my sincere gratitude to my supervisor, Professor Rogério Tenreiro, for giving me this opportunity and for all his support and guidance throughout the last year. I have truly learned immensely working with you. Also, I would like to show appreciation to my supervisor from IST, Professor Nuno Mira, for his support along the development of this thesis. I would also like to thank Professor Ana Tenreiro for all her time and help, especially with the flow cytometry assays. Additionally, I’d like to thank Professor Lélia Chambel for her help with the Bionumerics software. I would like to thank Filipa Antunes, from the Lab Bugworkers | M&B-BioISI, for the remarkable organization of the lab and for all her help. I would like to express my gratitude to Mendes Gonçalves, S.A. for the opportunity to carry out this thesis and for providing support during the whole course of this project. Special thanks to Cristiano Roussado for always being available. Also, a big thank you to my colleagues and friends, Catarina, Sofia, Tatiana, Ana, Joana, Cláudia, Mariana, Inês and Pedro for their friendship, support and for this enjoyable year, especially to Ana Marta Lourenço for her enthusiastic Gram stainings. -
Asaia Siamensis Sp. Nov., an Acetic Acid Bacterium in the Α-Proteobacteria
International Journal of Systematic and Evolutionary Microbiology (2001), 51, 559–563 Printed in Great Britain Asaia siamensis sp. nov., an acetic acid NOTE bacterium in the α-Proteobacteria Kazushige Katsura,1 Hiroko Kawasaki,2 Wanchern Potacharoen,3 Susono Saono,4 Tatsuji Seki,2 Yuzo Yamada,1† Tai Uchimura1 and Kazuo Komagata1 Author for correspondence: Yuzo Yamada. Tel\Fax: j81 54 635 2316. e-mail: yamada-yuzo!mub.biglobe.ne.jp 1 Laboratory of General and Five bacterial strains were isolated from tropical flowers collected in Thailand Applied Microbiology, and Indonesia by the enrichment culture approach for acetic acid bacteria. Department of Applied Biology and Chemistry, Phylogenetic analysis based on 16S rRNA gene sequences showed that the Faculty of Applied isolates were located within the cluster of the genus Asaia. The isolates Bioscience, Tokyo constituted a group separate from Asaia bogorensis on the basis of DNA University of Agriculture, 1-1-1 Sakuragaoka, relatedness values. Their DNA GMC contents were 586–597 mol%, with a range Setagaya-ku, Tokyo of 11 mol%, which were slightly lower than that of A. bogorensis (593–610 156-8502, Japan mol%), the type species of the genus Asaia. The isolates had morphological, 2 The International Center physiological and biochemical characteristics similar to A. bogorensis strains, for Biotechnology, but the isolates did not produce acid from dulcitol. On the basis of the results Osaka University, 2-1 Yamadaoka, Suita, obtained, the name Asaia siamensis sp. nov. is proposed for these isolates. Osaka 568-0871, Japan Strain S60-1T, isolated from a flower of crown flower (dok rak, Calotropis 3 National Center for gigantea) collected in Bangkok, Thailand, was designated the type strain Genetic Engineering and ( l NRIC 0323T l JCM 10715T l IFO 16457T). -
Kefir As a Functional Beverage Gaining Momentum Towards Its
beverages Review Kefir as a Functional Beverage Gaining Momentum towards Its Health Promoting Attributes Vassilios Ganatsios 1 , Poonam Nigam 2, Stavros Plessas 3 and Antonia Terpou 4,* 1 Department of Agricultural Biotechnology and Oenology, International Hellenic University, 66100 Drama, Greece; [email protected] 2 Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK; [email protected] 3 Laboratory of Food Processing, Faculty of Agriculture Development, Democritus University of Thrace, 68200 Orestiada, Greece; [email protected] 4 Department of Agricultural Development, Agri-Food, and Natural Resources Management, School of Agri-Cultural Development, Nutrition & Sustainability, National and Kapodistrian University of Athens, 34400 Psachna, Greece * Correspondence: [email protected] Abstract: The consumption of fermented foods posing health-promoting attributes is a rising global trend. In this manner, fermented dairy products represent a significant subcategory of functional foods with established positive health benefits. Likewise, kefir—a fermented milk product manu- factured from kefir grains—has been reported by many studies to be a probiotic drink with great potential in health promotion. Existing research data link regular kefir consumption with a wide range of health-promoting attributes, and more recent findings support the link between kefir’s probiotic strains and its bio-functional metabolites in the enhancement of the immune system, pro- viding significant antiviral effects. Although it has been consumed for thousands of years, kefir Citation: Ganatsios, V.; Nigam, P.; has recently gained popularity in relation to novel biotechnological applications, with different Plessas, S.; Terpou, A. Kefir as a fermentation substrates being tested as non-dairy functional beverages. -
High-Level Classification of the Fungi and a Tool for Evolutionary Ecological Analyses
Fungal Diversity (2018) 90:135–159 https://doi.org/10.1007/s13225-018-0401-0 (0123456789().,-volV)(0123456789().,-volV) High-level classification of the Fungi and a tool for evolutionary ecological analyses 1,2,3 4 1,2 3,5 Leho Tedersoo • Santiago Sa´nchez-Ramı´rez • Urmas Ko˜ ljalg • Mohammad Bahram • 6 6,7 8 5 1 Markus Do¨ ring • Dmitry Schigel • Tom May • Martin Ryberg • Kessy Abarenkov Received: 22 February 2018 / Accepted: 1 May 2018 / Published online: 16 May 2018 Ó The Author(s) 2018 Abstract High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum- and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative. Based on phylogenies and divergence time estimates, we adopt phylum rank to Aphelidiomycota, Basidiobolomycota, Calcarisporiellomycota, Glomeromycota, Entomoph- thoromycota, Entorrhizomycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota and Olpidiomycota. We accept nine subkingdoms to accommodate these 18 phyla. We consider the kingdom Nucleariae (phyla Nuclearida and Fonticulida) as a sister group to the Fungi. We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework, using this or any other classification system. We provide an example