Kazunobu matsushita, hirohide toyama, naoto tonouchi, akiko okamoto kainuma (eds ) acetic acid bacteria ecology and physiology springer japan (2016)

Kazunobu Matsushita · Hirohide Toyama Naoto Tonouchi · Akiko OkamotoKainuma Editors Acetic Acid Bacteria Ecology and Physiology Acetic Acid Bacteria ThiS is a FM Blank Page Kazunobu Matsushita • Hirohide Toyama • Naoto Tonouchi • Akiko Okamoto-Kainuma Editors Acetic Acid Bacteria Ecology and Physiology Editors Kazunobu Matsushita Department of Biological Chemistry, Faculty of Agriculture Yamaguchi University Yamaguchi Japan Naoto Tonouchi Bio-Fine Research Institute Ajinomoto Co Inc Kawasaki Japan Hirohide Toyama Department of Bioscience and Biotechnology, Faculty of Agriculture University of the Ryukyus Okinawa Japan Akiko Okamoto-Kainuma Department of Fermentation Science, Faculty of Applied Bioscience Tokyo University of Agriculture Tokyo Japan ISBN 978-4-431-55931-3 ISBN 978-4-431-55933-7 DOI 10.1007/978-4-431-55933-7 (eBook) Library of Congress Control Number: 2016940902 © Springer Japan 2016 This work is subject to copyright All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed The use of general descriptive names, registered names, trademarks, service marks, etc in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer Japan KK Preface Research for acetic acid bacteria (AAB) has a long history since the discovery of AAB by Louis Pasteur and its identification by Martinus Beijerinck in the nineteenth century In the twentieth century, basic research on the taxonomic study of AAB and on biochemical study for the unique oxidative reactions of AAB progressed as did the industrial applications of AAB not only in vinegar fermentation but also in the bioconversion process for useful chemical or pharmaceutical products Entering the twenty-first century, AAB research has continued to expand and is expected to show further progress in all aspects of AAB: classification and ecology, physiology and biochemistry, genetics, and biotechnology of vinegar fermentation and other oxidative fermentations The research on AAB has developed significantly in the last decade, which makes these bacteria more valuable for various industrial uses Readers can obtain useful, comprehensive information which is exciting with regard to basic science and provides suggestions for better application of these bacteria to a variety of practical production processes as well In order to view the future targets or directions of AAB research, we would like to summarize the distinctive physiological properties of AAB and the recent progress on AAB study, especially in the following areas (1) Molecular phylogeny and genome study of AAB; (2) Ecological features of AAB: interaction with plants, natural fermentation systems, and insects; (3) Physiological features and living strategies of AAB: rapid oxidation ability, acid resistance, biofilm formation, and genetic instability, and others; (4) Molecular mechanisms of several oxidative fermentations: acetate fermentation, sorbose fermentation, ketogluconate fermentation, and others; (5) Recent biotechnological aspects of AAB: biocatalysts, biosensors, biofuel cells, biocellulose, other useful polysaccharides, and so on Yamaguchi, Japan Kazunobu Matsushita v ThiS is a FM Blank Page Contents Systematics of Acetic Acid Bacteria Yuzo Yamada Acetic Acid Bacteria in Production of Vinegars and Traditional Fermented Foods Yoshikatsu Murooka Acetic Acid Bacteria in Fermented Food and Beverage Ecosystems Vasileios Pothakos, Koen Illeghems, David Laureys, Freek Spitaels, Peter Vandamme, and Luc De Vuyst 51 73 Acetic Acid Bacteria as Plant Growth Promoters 101 Rau´l O Pedraza Acetic Acid Bacteria as Symbionts of Insects 121 Elena Crotti, Bessem Chouaia, Alberto Alma, Guido Favia, Claudio Bandi, Kostas Bourtzis, and Daniele Daffonchio Drosophila–Acetobacter as a Model System for Understanding Animal–Microbiota Interactions 143 Sung-Hee Kim, Kyung-Ah Lee, Do-Young Park, In-Hwan Jang, and Won-Jae Lee Distribution, Evolution, and Physiology of Oxidative Fermentation 159 Kazunobu Matsushita and Minenosuke Matsutani Physiology of Acetobacter spp.: Involvement of Molecular Chaperones During Acetic Acid Fermentation 179 Akiko Okamoto-Kainuma and Morio Ishikawa vii viii Contents Physiology of Komagataeibacter spp During Acetic Acid Fermentation 201 Franc¸ois Barja, Cristina Andre´s-Barrao, Ruben Ortega Pe´rez, Elena Marı´a Cabello, and Marie-Louise Chappuis 10 Physiology of Acetobacter and Komagataeibacter spp.: Acetic Acid Resistance Mechanism in Acetic Acid Fermentation 223 Shigeru Nakano and Hiroaki Ebisuya 11 Central Carbon Metabolism and Respiration in Gluconobacter oxydans 235 Stephanie Bringer and Michael Bott 12 Metabolic Features of Acetobacter aceti 255 Hiroyuki Arai, Kenta Sakurai, and Masaharu Ishii 13 Membrane-Bound Dehydrogenases of Acetic Acid Bacteria 273 Osao Adachi and Toshiharu Yakushi 14 Cellulose and Other Capsular Polysaccharides of Acetic Acid Bacteria 299 Naoto Tonouchi 15 Industrial Application of Acetic Acid Bacteria (Vitamin C and Others) 321 Masako Shinjoh and Hirohide Toyama Appendix 339 Index 345 Chapter Systematics of Acetic Acid Bacteria Yuzo Yamada Abstract Acetic acid bacteria are currently accommodated in the acetous group, the family Acetobacteraceae, the class Alphaproteobacteria, based on phylogeny, physiology, and ecology The acetic acid bacteria are classified at present in 17 genera, of which many species have been reported in the genera Acetobacter, Gluconobacter, Gluconacetobacter, Asaia, and Komagataeibacter Of the remaining 12 genera, Acidomonas, Kozakia, Swaminathania, Saccharibacter, Neoasaia, Granulibacter, Tanticharoenia, Ameyamaea, Endobacter, Nguyenibacter, and Swingsia are monotypic; the genus Neokomagataea contains two species In the class Gammaproteobacteria, the genus Frateuria has been mentioned taxonomically as pseudacetic acid bacteria In addition, isolation and identification of acetic acid bacteria are described Keywords Acetic acid bacteria • Acetobacteraceae • Alphaproteobacteria • The acetous group • Acetobacter • Acetobacter aceti • Gluconobacter • Gluconobacter oxydans • Pseudacetic acid bacteria • Gammaproteobacteria • Frateuria 1.1 Introduction The generic name Acetobacter, the oldest name for acetic acid bacteria, was introduced by Beijerinck (1898) However, there is no record of the formal proposal of the generic name as a genus (Komagata et al 2014; Buchanan et al 1966; Kluyver 1983) Skerman et al (1980) cited, ‘as it occurs today’ in the Approved Lists of Bacterial Names 1980, the generic name Acetobacter as Acetobacter Beijerinck 1898, in which the type species was designated as Acetobacter aceti (Pasteur 1864) Beijerinck 1898 Asai (1935) divided the acetic acid bacteria into two genera: one genus included the species that oxidized ethanol more intensely than D-glucose and had the Y Yamada (*) Department of Applied Biological Chemistry, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan e-mail: yamada333@kch.biglobe.ne.jp © Springer Japan 2016 K Matsushita et al 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pathway from sorbose to 2-keto-L-gulonic acid Biotechnol Bioeng 14:1035–1038 Yamada K, Kodama T, Obata T, Takahashi N (1971) Microbial formation of tartaric acid from glucose: (I) Isolation and identification of tartaric acid producing microorganisms Hakko Kougaku Kaishi 49:85–92 (in Japanese) Appendix Summary of changes in names of Acetic Acid Bacteria (AAB) in each chapter Strain names that appeared in each chapter: those not used now Names originally used Chapter Names used previously but further changed Names presently used Strain names that appeared in each chapter: those presently used Acetobacter liquefaciens Gluconacetobacter liquefaciens Acetobacter cerevisiae Acetobacter fabarum ‘Acetobacter polyoxogenes’ ‘Komagataeibacter polyoxogenes’ Acetobacter ghanensis Acetobacter indonesiensis Acetobacter xylinum Gluconacetobacter xylinusa Komagataeibacter xylinus Acetobacter lambici Acetobacter malorum Acetobacter europaeus Gluconacetobacter europaeus Komagataeibacter europaeus Acetobacter orientalis Acetobacter orleanensis Acetobacter hansenii Gluconacetobacter hansenii Komagataeibacter hansenii Acetobacter pasteurianus Acetobacter pomorum Gluconacetobacter intermedius Komagataeibacter intermedius Acetobacter senegalensis Acetobacter sicerae Gluconacetobacter kakiaceti Komagataeibacter kakiaceti Acetobacter syzygii Acetobacter tropicalis Gluconacetobacter maltaceti Komagataeibacter maltaceti ‘Acetobacter rancens’ Acetobacter lovaniensis Gluconacetobacter medellinensis Komagataeibacter medellinensis Gluconobacter frateurii Gluconacetobacter sacchari Gluconacetobacter oboediens Komagataeibacter oboediens ‘Gluconacetobacter intermedius subsp tamanoi’ Gluconobacter suboxydans Gluconobacter oxydans Gluconobacter oxydans subsp sphaericus Gluconobacter sphaericus (continued) © Springer Japan 2016 K Matsushita et al (eds.), Acetic Acid Bacteria, DOI 10.1007/978-4-431-55933-7 339 340 Appendix Strain names that appeared in each chapter: those not used now Names originally used Chapter Names presently used Strain names that appeared in each chapter: those presently used Gluconobacter melanogenus IFO3293 Gluconobacter oxydans NBRC3293 Gluconobacter oxydans Gluconobacter oxydans 621H Gluconacetobacter oboediens Komagataeibacter oboediens Gluconobacter oxydans H24 Komagataeibacter xylinus Gluconacetobacter saccharivorans Komagataeibacter saccharivorans Komagataeibacter medellinensis Komagataeibacter intermedius Komagataeibacter kombuchae Komagataeibacter hansenii Gluconacetobacter diazotrophicus Acetobacter aceti Gluconobacter oxydans DSM3504 Acetobacter aceti NBRC14818 Acetobacter pasteurianus NBRC3283 Acetobacter pasteurianus 386B Acetobacter pasteurianus Acidiphilium cryptum Acidiphilium multivorum Gluconacetobacter sacchari Gluconobacter japonicus Acetobacter pasteurianus NBRC3191 Acetobacter pasteurianus NBRC101655 Acetobacter pasteurianus SKU1108 Acetobacter tropicalis SKU1100 Acetobacter nitrogenifigens Acetobacter syzygii Acetobacter lovaniensis Acetobacter fabarum Acetobacter cerevisiae Acetobacter ghanensis Acetobacter sicerae Acetobacter malorum Gluconacetobacter diazotrophicus Gluconacetobacter azotocaptans Gluconacetobacter johannae Acetobacter nitrogenifigens Swaminathania salitolerans Acetobacter peroxydans Gluconacetobacter kombuchae Chapter Names used previously but further changed Gluconacetobacter kombuchae (LMG23726T) Gluconacetobacter hanseniib Gluconacetobacter hanseniib Komagataeibacter kombuchae (continued) Appendix 341 Strain names that appeared in each chapter: those not used now Chapter Names originally used Names used previously but further changed Names presently used Strain names that appeared in each chapter: those presently used Gluconacetobacter kombuchae Gluconacetobacter hanseniib Komagataeibacter kombuchae Acetobacter aceti Acetobacter nitrogenifigens Acetobacter peroxydans Acetobacter pomorum Acetobacter tropicalis Asaia astilbes Chapter Asaia bogorensis Asaia platycodi Commensalibacter intestini Gluconacetobacter diazotrophicus Gluconobacter frateurii Gluconobacter morbifer Gluconobacter oxydans Gluconobacter thailandicus Granulibacter bethesdensis Komagataeibacter europaeus Komagataeibacter hansenii Komagataeibacter nataicola Komagataeibacter oboediens Komagataeibacter rhaeticus Komagataeibacter swingsii Komagataeibacter xylinus Saccharibacter floricola Swaminathania salitolerans Commensalibacter intestini Gluconobacter morbifer Acetobacter pomorum Chapter Acetobacter methanolicus Acidomonas methanolica Acetobacter pasteurianus Acidiphilium cryptum Acetobacter aurantius Frateuria aurantia (not AAB) Gluconacetobacter diazotrophicus Gluconobacter oxydans Granulibacter bethesdensis Chapter Acetobacter aceti IFO 3283 Acetobacter aceti DSMZ 2002 Acetobacter sp NBRC 3283 Acetobacter pasteurianus NBRC 3283 Acetobacter pasteurianus LMG 1262 Acetobacter aceti DSM 2002 (continued) 342 Appendix Strain names that appeared in each chapter: those not used now Names originally used Chapter Names presently used Strain names that appeared in each chapter: those presently used Gluconacetobacter europaeus Komagataeibacter europaeus Acetobacter pasteurianus Gluconacetobacter hansenii Komagataeibacter hansenii Gluconacetobacter entanii Gluconacetobacter intermedius Komagataeibacter intermedius Gluconacetobacter kakiaceti Komagataeibacter kakiaceti Gluconacetobacter kombuchae Chapter 10 Names used previously but further changed Gluconacetobacter hanseniib Komagataeibacter maltaceti Gluconacetobacter medellinensis Komagataeibacter medellinensis Gluconacetobacter nataicola Komagataeibacter nataicola Gluconacetobacter oboediens Komagataeibacter oboediens Gluconacetobacter rhaeticus Komagataeibacter rhaeticus Gluconacetobacter saccharivorans Komagataeibacter saccharivorans Gluconacetobacter sucrofermentans Komagataeibacter sucrofermentans Gluconacetobacter swingsii Komagataeibacter swingsii Gluconacetobacter xylinus Komagataeibacter xylinus Acetobacter sp NBRC 3283 (¼ IFO 3283) ‘Acetobacter polyoxogenes’ Acetobacter europaeus Chapter 11 Komagataeibacter kombuchae Gluconacetobacter maltaceti Acetobacter aceti (IFO3283) Acetobacter malorum S24 Acetobacter pasteurianus NBRC 3283 (¼ IFO 3283) ‘Komagataeibacter polyoxogenes’ Gluconacetobacter europaeus Komagataeibacter europaeus Gluconobacter melanogenus IFO3293 Gluconobacter oxydans NBRC3293 Gluconobacter oxydans Gluconobacter oxydans 621H Gluconacetobacter oboediens Komagataeibacter oboediens Acetobacter pasteurianus IFO3283-01 Gluconacetobacter diazotrophicus PAl5 Gluconacetobacter xylinus Komagataeibacter xylinus Acetobacter aceti Gluconobacter oxydans DSM3504 Acetobacter aceti NBRC14818 Acetobacter pasteurianus NBRC3283 Acetobacter pasteurianus 386B (continued) Appendix 343 Strain names that appeared in each chapter: those not used now Names originally used Chapter 12 Names used previously but further changed Gluconacetobacter xylinus I 2281 Names presently used Strain names that appeared in each chapter: those presently used Komagataeibacter medellinensis Acetobacter aceti NBRC 14818 Acetobacter pasteurianus NBRC 3283 Gluconacetobacter diazotrophicus Gluconobacter oxydans Granulibacter bethesdensis Chapter 13 Chapter 14 Chapter 15 a Acetobacter europaeus Gluconacetobacter europaeus Komagataeibacter europaeus Gluconacetobacter diazotrophicus Acetobacter liquefaciens Gluconacetobacter liquefaciens Gluconacetobacter liquefaciens RCTMR Gluconobacter industrius IFO 3260 Gluconobacter japonicus NBRC 3260 Gluconobacter oxydans IFO 3244 Gluconobacter melanogenus Gluconobacter oxydans Gluconobacter oxydans NBRC 12528 Gluconobacter oxydans DSM4025 Ketogulonicigenium vulgare (not AAB) Acetobacter xylinum subsp sucrofermentans Komagataeibacter sucrofermentans BPR2001 Acetobacter xylinum subsp nonacetooxidans Komagataeibacter swingsii Acetobacter aceti subsp xylinum Komagataeibacter xylinus Gluconobacter oxydans NBRC 3292 Acetobacter liquefaciens IFO 12258 Gluconacetobacter liquefaciens NBRC 12258 Acetobacter orientalis KYG22 Gluconobacter melanogenus IFO 3293 Gluconobacter oxydans NBRC 3293 Gluconobacter melanogenus UV10 Gluconobacter oxydans UV10 Gluconobacter melanogenus ATCC9937 Gluconobacter oxydans ATCC9937 Gluconobacter oxydans IFO3255 Gluconobacter thailandicus NBRC3255 Gluconobacter suboxydans Gluconobacter oxydans Gluconobacter suboxydans IFO 3291 Gluconobacter thailandicus NBRC3291 Gluconobacter suboxydans IFO12528 Gluconobacter oxydans NBRC12528 Acetobacter pasteurianus (strain NBRC3284) Ketogulonicigenium vulgare DSM4025 In some references, mistakenly used as Ga xylinum Gluconacetobacter kombuchae is a later heterotypic synonym of Gluconacetobacter hansenii Cleenwerck et al (2009) b Index A AarA See Citrate synthase (AarA) Acetan (AM-2), 306 Acetate CoA-trasferase (AarC), 227, 228 Acetate overoxidation, 256, 261, 262, 264–268 Acetic acid, 145, 149 bacteria, 74–91 fermentation, 179–196, 202–216 tolerance, 224, 226, 228, 229, 232–233 Acetobacter A aceti, 1, 2, 9, 10, 43, 56, 59–62, 64, 66, 80, 83, 84, 89, 180, 186 A cerevisiae, 59 A europaeus, 58 A fabarum, 63 A ghanensis, 63 A hansenii, 60 A indonesiensis, 65 A lambici, 66, 87 A liquefaciens, 60 A lovaniensis, 65 A malorum, 59, 62, 65 A nitrogenifigens, 103–106 A oboediens, 58 A orientalis, 65, 334 A pasteurianus, 52, 53, 56–63, 65–67, 79, 84, 88, 89, 91, 171, 180–186, 188–190, 192–196 A peroxydans, 103–105, 115 A polyoxogenes, 52 A pomorum, 58, 65 A senegalensis, 63 A sicerae, 60 A syzygi, 65 A tropicalis, 61, 65, 77, 89, 333 © Springer Japan 2016 K Matsushita et al (eds.), Acetic Acid Bacteria, DOI 10.1007/978-4-431-55933-7 A xylinum, 52 Acetobacteraceae, 3, 9, 146–148, 151–155 Acetous group, 3, Acidic beer, 74, 85–87 Acidiphilium, 163, 164, 166 Acidomonas, 2, 3, 19–20, 40 A methanolica, 20, 163 Aconitase, 228, 230–232 Adaptive evolution, 161–168 Aerobic submerged fermentation, 224, 225 Agitation cultures, 307–310 Alcohol dehydrogenase (ADH), 162, 163, 169, 224, 256, 277–280, 282, 284, 327 Aldehyde dehydrogenase (ALDH), 224, 225, 232, 256, 258, 262, 263, 265, 267, 277–280, 284 Alphaproteobacteria, 3, Ameyamaea, 3, 31–32 A chiangmaiensis, 32 Amino acids, 212–213 Analogue-resistant mutants, 308 Antagonistic effects against pathogens, 111 Application in agriculture, 114–115 Artificial skin, 313 Asaia, 3, 5, 23–27, 29 A bogorensis, 5, 24 Aspergillus oryzae, 52 ATP-binding cassette (ABC) transporter, 229, 231–233 B Bacillus megaterium, 325 Bacterial cellulose synthesis (BCS), 302–304 345 346 Balsamic vinegar, 58–59, 62 Betaproteobacteria, 163, 167, 170–173 Beer, 81, 85–87, 90 Bertrand-Hudson’s rule, 325 Betainaldehyde dehydrogenase, 327 Beverage fermentation, 74, 78 Biodiesel fuel (BDF), 333 Biofilm, 305, 306 Biological nitrogen fixation, 105, 106, 108, 109 Biomass production, 249 Biomass yield, 249 Bio-Polymer Research Co Ltd (BPR), 307 Biostimulants, 112 Biotechnological applications, 112 BPR2001, 302, 308, 309 Bumblebees, 127, 128 C Caspian Sea Yogurt, 65, 334 ccmC, 149, 151 ccmF, 149, 151 ccmH, 149, 151 CcpAx (ORF-2), 303, 304 Cell–cell interaction, 305 Cell morphology, 208–212 Cellulose, 122, 128, 129, 132, 299–315 Cellulose synthase complex, 302, 304 Cell yield, 244, 249 Chagas disease, 136 Chaperones, 231–233 Citrate synthase (AarA), 227, 228, 231, 232 ClpB, 181, 182, 186, 191–195 13 C-Metabolic flux analyses, 240–242 Cocoa bean fermentation, 74–79, 89–91 Cocoa bean heap, 63 Commensal bacteria, 151, 153 Commensals, 124, 125 ctaD, 149, 151 cyaA, 149, 151 Cyanide-insensitive oxidase (CIO), 161, 173–175, 242, 244 Cyclic carbon flux, 241 Cyclic di-GMP (c-di-GMP), 304 Cytochrome, 277–281 bc1 complex, 247–249 bd oxidase, 173, 174 bo3 oxidase, 170–172, 244, 245, 248 oxidases, 129 Cytochrome c oxidase (COX), 170–173, 175, 247, 248 Cytosolic proteins, 214 Index D D-adonitol, 325 D-arabitol, 325 Dekkera bruxellensis, 82, 86, 87 Delta-Notch, 153 Denaturing gradient gel electrophoresis (DGGE), 52, 56 Developmental rate, 132 Dextran, 334 Dextrin dextranase, 334 D-fructose, 325 D-gluconate dehydrogenase (GADH), 327 D-glucose, 323, 324, 329, 331 dehydrogenase, 326 Dihydroxyacetone, 325, 330, 333 2,5-diketo-D-gluconic acid, 323, 324, 329, 330 Disintegrated bacterial cellulose, 311–312, 314 Dispersed suspension, 310 D-mannitol, 325, 326 DNA–DNA hybridization, 6, DNA G+C content, 10–43 DnaJ (dnaJ), 186–190, 195 DnaK (dnaK), 182, 187–195 D-ribulose, 325 Drosophila, 125, 126, 134, 137, 143–155 dsbD, 149, 151 D-sorbitol, 322–330 dehydrogenase, 325, 326 Dual oxidase (DUOX), 151–153 D-xylulose, 325 E Ecology, 102–105 Ecosystem, 74–91 Efflux pump, 230–233 Embden–Meyerhof–Parnas (EMP) pathway, 236, 257 Endobacter, 3, 39 E medicaginis, 39 Engineered symbiont, 136 Enrichment culture approach, Enterobacteriaceae, 86, 87 Enterobacterial repetitive intergenic consensus -polymerase chain reaction (ERICPCR), 52, 53 Enteroblast (EB), 153, 154 Enterocytes (EC), 153, 154 Enteroendocrine cells (EEC), 153 Entner–Doudoroff pathway (EDP), 236, 237, 240 Environmental acquisition, 131 Index Epithelial cell renewal (ECR) program, 153, 154 Erythrulose, 325 Evolution, 124, 129, 134 F F1Fo-type ATP synthases, 245 FAD-SLDH, 326 FAD-2KGADH, 327 Fig vinegar, 61 Flavin adenine dinucleotide (FAD), 281, 284 Flavoprotein, 162, 166–168, 174, 175, 277, 280–281, 284 Food fermentation, 88, 91 Forkhead transcription factor (dFOXO), 151 Frateuria, 42–43 F aurantia, 2, 42, 43, 165 Fructan, 334 Fructose, 301, 302, 308 Fukuyama kurozu, 56, 57 G Gammaproteobacteria, 42, 163, 167, 170–173 Gas chromatography-mass spectrometry (GC-MS), 64 Genetic characteristics, 102, 107–108 Gengiflex, 313 Genome, 123, 128, 133–135 Genome of G diazotrophicus PAL5, 108 Genomic, 87, 88, 203, 214–216 Gibberellins, 109, 110 Gluconacetobacter Ga azotocaptans, 103–105, 110 Ga diazotrophicus, 103, 107, 113, 174 Ga hansenii, 59 Ga intermedius, 53 Ga intermedius subsp tamanoi, 53 Ga johannae, 103–105, 110 Ga kakiaceti, 62 Ga kombuchae, 103–105 Ga liquefaciens, 21, 60, 327 Ga maltaceti, 62 Ga medellinensis, 63 Ga polyoxogenes, 52 Ga sacchari, 59 Gluconobacter G cerevisiae, 87 G cerinus, 334 G frateurii, 65, 326, 333, 334 G liquefaciens, 2, 3, 20, 21 347 G oxydans, 2, 15, 16, 53, 66, 162, 323–331, 333, 334 G oxydans subsp sphaericus, 53 G sphaericus, 53 G thailandicus, 325–327 Glucose dehydrogenase (GDH), 281–284, 288 Glucose 6-phosphate dehydrogenase, 236, 237 Glutaraldehyde, 327 Glyceric acid (GLA), 333 Glycerol, 325–327, 330, 333 Glycerol dehydrogenase (GLDH), 281–284, 326, 330 Glycolaldehyde, 327, 332 Glycolic acid, 332 Glyoxal, 327 Glyoxylate cycle, 236, 243, 249 Glyoxylate pathway, 257, 261–263, 265–269 Gnotobiotic animals, 145–147, 149 Granulibacter, 3, 30, 163, 166, 173 G bethesdensis, 30 GroE (groE), 190, 193 Growth phases, 241, 242 GrpE (grpE), 186–190, 192, 194, 195 Gut, 124, 125, 127–129, 131, 133, 134, 136, 138 H H+/O ratio, 244, 245 Heat shock, 185, 189, 192–195 Heme, 277, 278, 281 Heme-copper oxidase, 170 High-throughput sequencing, 86 Holobiont, 145 Honeybees, 123, 127, 128, 138 Horizontal gene transfer (HGT), 165, 166, 168, 170, 171, 174, 175 Horizontal transmissions, 131 Host–vector system, 309 Hypothetical membrane protein (hmp), 149, 151 I Immune system, 123–125, 133, 137, 138 Indole-3-acetic acid (IAA), 107, 109, 110 Inoculants and inoculation, 112–113 Inositol dehydrogenase, 329 Insects, 122–138 Insulin/IGF signaling (IIS) pathways, 149 Insulin-like growth factors (IGF), 149 Insulin-like peptides (ILP), 149, 151 Insulin producing cells (IPCs), 149, 151, 152 348 Intestinal stem cell (ISC), 153, 154 Isocitrate lyase, 257, 261, 265 J JAK-STAT signaling, 153 Jerez vinegar, 59 K Kaki vinegar, 62 kasuzu, 52–56 Kefir, 80 2-keto-D-gluconate dehydrogenase, 327 2-keto-D-gluconic acid (2-KGA), 330 Ketogulonicigenium vulgare, 325, 326, 328 2-keto-L-gulonic acid (2KLGA), 323–330 2-keto-3-deoxy-6-phosphogluconate aldolase, 237, 243 4-keto-D-arabonate (4KAB), 289–291 5-keto-D-gluconic acid (5-KGA), 323, 324, 329–331 4-keto-D-ribonate, 291, 292 Kitora Tumulus, 66 koji mold, 51, 52, 56, 57 Komagataeibacter K europaeus, 58–60, 62, 67 K hansenii, 59 K intermedius, 53, 61 K kakiaceti, 62 K maltaceti, 62 K medellinensis, 63 K oboediens, 58, 61, 67 K xylinus, 3, 34, 35, 52, 56, 59, 60, 63, 323 Kombucha, 78, 83–85, 90 tea, 103–105 Komesu, 52–53 Kozakia, 3, 26–27, 29 K baliensis, 26, 65, 334 L Lactic acid bacteria, 74, 76–82, 84, 86, 87, 145 Lactobacillus, 77, 80, 82, 86 L acetotolerans, 56 Lactobionic acid (LBA), 333–334 Lactose, 333 Lambic beers, 78, 85–87 L-ascorbic acid, 321–330 Leafhopper, 127–129, 131, 132, 137 Leuconostoc, 80, 82 L mesenteroides, 334 Levan, 334 Index Levansucrase, 334 L-gulono-γ-lactone, 328 L-gulose, 328 L-idonic acid, 323, 324, 330 Lipidomics, 216 Lipids, 208, 211, 212 L-sorbose, 322–325, 327–330 L-sorbose dehydrogenase, 324 L-sorbose reductase (SR), 327 L-sorbosone, 323, 324, 327–329 L-sorbosone dehydrogenase (SNDH), 326–328 M Malaria, 127–129, 131–133, 135–137 Malate synthase, 257, 261, 265 Malt vinegar, 59 Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), 60, 67, 86 Mechanisms, 203, 213–215 Membrane lipid, 211, 213 Meso-erythritol, 325 Metabolic engineering, 249 Metagenetics, 89 Metagenomics, 87, 89 Microbial succession, 76, 85–87 Microbiome, 123–127, 137 Microfibrils, 300, 304, 310, 312 Milk kefir, 74, 79–82, 90 Mineral nutrients solubilization, 110–111 Miso, 64–65 Molecular chaperone, 179–196 Molybdoprotein, 162, 168, 277, 280 Molybdopterin cytosine dinucleotide (MCD), 280, 284 Mosquitoes, 123, 127–129, 131–137 N NADH dehydrogenase, 258, 263 Nata de coco, 63, 312 Neoasaia, 3, 29 N chiangmaiensis, 29, 334 Neokomagataea, 3, 9, 28, 32–33, 41 N thailandica, 33 Next-generation sequencing, 88 Nguyenibacter, 3, 39–40 N vanlangensis, 40 nif genes, 107 Nitrogenase nifHDK, 109 Nitrogen-fixing AAB, 102–103 Nitrogen-fixing bacteria, 132 Index O Olive fruit fly, 126, 127 Onion vinegar, 61 oprM, 149, 151 Overflow metabolism, 263, 267, 269 Oxidative fermentation, 159–175, 179, 182 Oxygen deprivation, 246 P Papermaking binder, 314 Pathobiont, 151–153 Pellicle, 299, 300, 305–307, 312 Pentose, 282, 288–289, 291, 292 Pentose phosphate pathway (PPP), 236, 237, 240–243, 258, 262 Periplasmic pyrroloquinoline quinone (PQQ), 149–152 Periplasmic respiration, 160, 161 Phosphate-solubilizing, 114 Phosphatidylcholine (PC), 226, 227, 232 Phosphatidylethanolamine, 226 Phosphatidylglycerol (PG), 226 6-phosphofructokinase, 236 6-phosphogluconate dehydratase, 237 6-phosphogluconate dehydrogenase, 236, 237 Phosphoglucose isomerase, 237, 242 Phylogenetic tree, 163, 164, 166–169, 172, 174 Phylogeny, 134, 135 Physiological characteristics, 105–107 Phytohormones, 108–110, 115 Pierce’s disease, 137 Plant growth-promoting bacteria (PGPB), 102, 103, 109, 110, 112, 114–116 Plasmids, 107, 108, 203, 215 Polysaccharide, 208–211, 226, 227, 232 Pot vinegar, 56 PQQ See Pyrroloquinoline quinone (PQQ) PQQ-ADH, 150 pqqB, 149, 151 pqqC, 149, 151 pqqE, 149, 151 PQQ-GDH, 330, 334 PQQ-GLDH, 324–326, 330 Primary symbionts, 124, 133 Proteomic analysis, 186, 190 Pseudacetic acid bacteria, 41–43 Pyridine nucleotide transhydrogenase, 242, 247 Pyrroloquinoline quinone (PQQ), 77, 160, 162, 163, 165, 166, 212, 213, 256, 258, 262–264, 268, 277, 278, 280, 281, 283, 284, 292, 326, 328–330, 333 Pyruvate decarboxylase, 263, 267 349 Q Quinate, 283, 285, 286, 288 Quinate dehydrogenase (QDH), 283, 285–288 Quinohemoprotein, 162, 163, 165, 168 Quinoprotein, 160–166, 174, 175, 277, 279, 281–283, 326, 329 R Random amplified polymorphic DNA (RAPD) methods, 52 Reactive oxygen species (ROS), 151, 265 Reduced genome, 124 Reichstein process, 322, 323, 329 Reproductive manipulators, 124 Reproductive organs, 127, 129, 131, 136 Resistance, 180, 186, 193, 195, 196, 203, 210–216 Respiratory chain, 160, 170–175, 224, 274, 277, 282 Restriction fragment length polymorphism (RFLP), 59 Ribbon, 300, 303, 310 RNA-seq, 185, 186, 192 RpoH (rpoH), 181, 183, 184, 186, 188, 189, 191, 193–196 S Saccharibacter, 3, 9, 28 S floricola, 28 Saccharococcus sacchari, 105 Saccharomyces cerevisiae, 52 Sake lee vinegar, 53–56 Sake yeast, 52 sboRA, 327 Secondary symbionts, 124, 125 Shikimate, 283, 285–288 Shoyu, 64 Siderophores, 111 Sigma 32, 183, 188, 191, 193–196 16S rRNA gene, 52, 61, 64, 65, 67, 86, 89–90 sldA, 326 sldB, 326 sldSLC, 326 Sorbose dehydrogenase (SDH), 327 Soy sauce, 64–65 Speaker diaphragm, 312–313 Spermidine, 110 Spontaneous fermentation, 85, 86 Squalene-hopene cyclase (shc), 149, 151 Stressors, 180–182, 185, 186, 190, 193, 195 Submerged fermentation (SF), 202, 205–207, 212–213 350 Succinyl-CoA:acetate CoA transferase (SCACT), 257, 258, 260 Sucrose, 308, 309, 334 Sucrose synthase, 309 Sugarcane, 103–106, 110, 111, 113–115 Surface fermentation, 224, 225 Swaminathania, 3, 27, 29 S salitolerans, 27, 103, 105 Swingsia, 3, 9, 28, 40–41 S samuiensis, 40–41 Symbiont-based control strategies, 123, 135–137 Symbionts, 122–138, 152, 153 Symbiosis, 123–125, 134 Symbiotic AAB, 125, 128 T Tanticharoenia, 3, 31 T sakaeratensis, 30–31 Tartaric acid, 330–332 Terminal complexes (TCs), 300, 304 Terminal oxidase, 224, 230 Tetragenococcus halophilus, 64 Tetrahydoxy-bacteriohopane (THBH), 226, 227 Thermotolerance, 79, 89 Toll-like receptors, 57 Transcriptome analyses, 236, 242–243 Transketolase, 332 Tricarboxylic acid (TCA) cycle, 236, 242, 243, 249 Tsubosu, 56–57, 60 Index Tsukemono, 64 Tumor necrosis factor (TNF)-α, 57 Two-dimensional gel electrophoresis (2-DE), 181–182, 186 U Ubiquinol oxidase (UOX), 161, 170–173, 175, 258 Ubiquinone (UQ), 274, 276–282, 285 UGP-glucose (UDPG), 301, 302 Ultrafine network, 300, 310 Uracil, 151, 153 V Vanadate, 332 Vertical transmission, 131 Vinegar, 51–67, 180, 196 Vitamin B, 132, 133 Vitamin C, 321–334 W Water kefir, 74, 81–83, 90 Wetland rice, 103, 105 Whole-genome sequencing, 88, 89 Y Yeasts, 74, 76–82, 84–87 Young’s modulus, 311, 312 .. .Acetic Acid Bacteria ThiS is a FM Blank Page Kazunobu Matsushita • Hirohide Toyama • Naoto Tonouchi • Akiko Okamoto- Kainuma Editors Acetic Acid Bacteria Ecology and Physiology Editors Kazunobu. .. Gammaproteobacteria, the genus Frateuria has been mentioned taxonomically as pseudacetic acid bacteria In addition, isolation and identification of acetic acid bacteria are described Keywords Acetic acid. .. 422-8529, Japan e-mail: yamada333@kch.biglobe.ne.jp © Springer Japan 2016 K Matsushita et al (eds. ), Acetic Acid Bacteria, DOI 10.1007/978-4-431-55933-7_1 Y Yamada capability of oxidizing acetic acid