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Román-Camacho JJ, García-García I, Santos-Dueñas IM, García-Martínez T, Mauricio JC. Latest Trends in Industrial Vinegar Production and the Role of Acetic Acid Bacteria: Classification, Metabolism, and Applications-A Comprehensive Review. Foods 2023; 12:3705. [PMID: 37835358 PMCID: PMC10572879 DOI: 10.3390/foods12193705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023] Open
Abstract
Vinegar is one of the most appreciated fermented foods in European and Asian countries. In industry, its elaboration depends on numerous factors, including the nature of starter culture and raw material, as well as the production system and operational conditions. Furthermore, vinegar is obtained by the action of acetic acid bacteria (AAB) on an alcoholic medium in which ethanol is transformed into acetic acid. Besides the highlighted oxidative metabolism of AAB, their versatility and metabolic adaptability make them a taxonomic group with several biotechnological uses. Due to new and rapid advances in this field, this review attempts to approach the current state of knowledge by firstly discussing fundamental aspects related to industrial vinegar production and then exploring aspects related to AAB: classification, metabolism, and applications. Emphasis has been placed on an exhaustive taxonomic review considering the progressive increase in the number of new AAB species and genera, especially those with recognized biotechnological potential.
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Affiliation(s)
- Juan J. Román-Camacho
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, 14014 Córdoba, Spain; (J.J.R.-C.); (T.G.-M.); (J.C.M.)
| | - Isidoro García-García
- Department of Inorganic Chemistry and Chemical Engineering, Agrifood Campus of International Excellence ceiA3, Nano Chemistry Institute (IUNAN), University of Córdoba, 14014 Córdoba, Spain;
| | - Inés M. Santos-Dueñas
- Department of Inorganic Chemistry and Chemical Engineering, Agrifood Campus of International Excellence ceiA3, Nano Chemistry Institute (IUNAN), University of Córdoba, 14014 Córdoba, Spain;
| | - Teresa García-Martínez
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, 14014 Córdoba, Spain; (J.J.R.-C.); (T.G.-M.); (J.C.M.)
| | - Juan C. Mauricio
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, 14014 Córdoba, Spain; (J.J.R.-C.); (T.G.-M.); (J.C.M.)
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2
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Zayed O, Hewedy OA, Abdelmoteleb A, Ali M, Youssef MS, Roumia AF, Seymour D, Yuan ZC. Nitrogen Journey in Plants: From Uptake to Metabolism, Stress Response, and Microbe Interaction. Biomolecules 2023; 13:1443. [PMID: 37892125 PMCID: PMC10605003 DOI: 10.3390/biom13101443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Plants uptake and assimilate nitrogen from the soil in the form of nitrate, ammonium ions, and available amino acids from organic sources. Plant nitrate and ammonium transporters are responsible for nitrate and ammonium translocation from the soil into the roots. The unique structure of these transporters determines the specificity of each transporter, and structural analyses reveal the mechanisms by which these transporters function. Following absorption, the nitrogen metabolism pathway incorporates the nitrogen into organic compounds via glutamine synthetase and glutamate synthase that convert ammonium ions into glutamine and glutamate. Different isoforms of glutamine synthetase and glutamate synthase exist, enabling plants to fine-tune nitrogen metabolism based on environmental cues. Under stressful conditions, nitric oxide has been found to enhance plant survival under drought stress. Furthermore, the interaction between salinity stress and nitrogen availability in plants has been studied, with nitric oxide identified as a potential mediator of responses to salt stress. Conversely, excessive use of nitrate fertilizers can lead to health and environmental issues. Therefore, alternative strategies, such as establishing nitrogen fixation in plants through diazotrophic microbiota, have been explored to reduce reliance on synthetic fertilizers. Ultimately, genomics can identify new genes related to nitrogen fixation, which could be harnessed to improve plant productivity.
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Affiliation(s)
- Omar Zayed
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 9250, USA;
- Genetics Department, Faculty of Agriculture, Menoufia University, Shebin El-Kom 32511, Egypt;
| | - Omar A. Hewedy
- Genetics Department, Faculty of Agriculture, Menoufia University, Shebin El-Kom 32511, Egypt;
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Ali Abdelmoteleb
- Botany Department, Faculty of Agriculture, Menoufia University, Shebin El-Kom 32511, Egypt;
| | - Mohammed Ali
- Maryout Research Station, Genetic Resources Department, Desert Research Center, 1 Mathaf El-Matarya St., El-Matareya, Cairo 11753, Egypt;
| | - Mohamed S. Youssef
- Botany and Microbiology Department, Faculty of Science, Kafrelsheikh University, Kafrelsheikh 33516, Egypt;
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ahmed F. Roumia
- Department of Agricultural Biochemistry, Faculty of Agriculture, Menoufia University, Shibin El-Kom 32514, Egypt;
| | - Danelle Seymour
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 9250, USA;
| | - Ze-Chun Yuan
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
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3
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Bittleston LS, Wolock CJ, Maeda J, Infante V, Ané JM, Pierce NE, Pringle A. Carnivorous Nepenthes Pitchers with Less Acidic Fluid House Nitrogen-Fixing Bacteria. Appl Environ Microbiol 2023; 89:e0081223. [PMID: 37338413 PMCID: PMC10370301 DOI: 10.1128/aem.00812-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/21/2023] Open
Abstract
Carnivorous pitcher plants are uniquely adapted to nitrogen limitation, using pitfall traps to acquire nutrients from insect prey. Pitcher plants in the genus Sarracenia may also use nitrogen fixed by bacteria inhabiting the aquatic microcosms of their pitchers. Here, we investigated whether species of a convergently evolved pitcher plant genus, Nepenthes, might also use bacterial nitrogen fixation as an alternative strategy for nitrogen capture. First, we constructed predicted metagenomes of pitcher organisms from three species of Singaporean Nepenthes using 16S rRNA sequence data and correlated predicted nifH abundances with metadata. Second, we used gene-specific primers to amplify and quantify the presence or absence of nifH directly from 102 environmental samples and identified potential diazotrophs with significant differential abundance in samples that also had positive nifH PCR tests. Third, we analyzed nifH in eight shotgun metagenomes from four additional Bornean Nepenthes species. Finally, we conducted an acetylene reduction assay using greenhouse-grown Nepenthes pitcher fluids to confirm nitrogen fixation is indeed possible within the pitcher habitat. Results show active acetylene reduction can occur in Nepenthes pitcher fluid. Variation in nifH from wild samples correlates with Nepenthes host species identity and pitcher fluid acidity. Nitrogen-fixing bacteria are associated with more neutral fluid pH, while endogenous Nepenthes digestive enzymes are most active at low fluid pH. We hypothesize Nepenthes species experience a trade-off in nitrogen acquisition; when fluids are acidic, nitrogen is primarily acquired via plant enzymatic degradation of insects, but when fluids are neutral, Nepenthes plants take up more nitrogen via bacterial nitrogen fixation. IMPORTANCE Plants use different strategies to obtain the nutrients that they need to grow. Some plants access their nitrogen directly from the soil, while others rely on microbes to access the nitrogen for them. Carnivorous pitcher plants generally trap and digest insect prey, using plant-derived enzymes to break down insect proteins and generate a large portion of the nitrogen that they subsequently absorb. In this study, we present results suggesting that bacteria living in the fluids formed by Nepenthes pitcher plants can fix nitrogen directly from the atmosphere, providing an alternative pathway for plants to access nitrogen. These nitrogen-fixing bacteria are only likely to be present when pitcher plant fluids are not strongly acidic. Interestingly, the plant's enzymes are known to be more active under strongly acidic conditions. We propose a potential trade-off where pitcher plants sometimes access nitrogen using their own enzymes to digest prey and at other times take advantage of bacterial nitrogen fixation.
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Affiliation(s)
- Leonora S. Bittleston
- Department of Biological Sciences, Boise State University, Boise, Idaho, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Charles J. Wolock
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Junko Maeda
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Valentina Infante
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Agronomy, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Naomi E. Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
| | - Anne Pringle
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Botany, University of Wisconsin—Madison, Madison, Wisconsin, USA
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4
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Vio SA, Galar ML, Gortari MC, Balatti P, Garbi M, Lodeiro AR, Luna MF. Multispecies Bacterial Bio-Input: Tracking and Plant-Growth-Promoting Effect on Lettuce var. sagess. PLANTS (BASEL, SWITZERLAND) 2023; 12:736. [PMID: 36840083 PMCID: PMC9962684 DOI: 10.3390/plants12040736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
The use of multispecies bacterial bio-inputs is a promising strategy for sustainable crop production over the use of single-species inoculants. Studies of the use of multispecies bio-inputs in horticultural crops are scarce, not only on the growth-promoting effects of each bacterium within the formulation, but also on their compatibility and persistence in the root environment. In this work, we described that a multispecies bacterial bio-input made up of Azospirillum argentinense Az39, Gluconacetobacter diazotrophicus PAL-5, Pseudomonas protegens Pf-5 and Bacillus sp. Dm-B10 improved lettuce plant growth more effectively than when these strains were inoculated as single-species bio-inputs. Bacteria persisted together (were compatible) and also colonized seedling roots of lettuce plants grown in controlled conditions. Interestingly, colonization was highly related to an early and enhanced growth of seedlings grown in the nursery. A similar effect on plant growth was found in lettuce plants in a commercial greenhouse production in the peri-urban area of La Plata City, Buenos Aires, Argentina. To our knowledge, this is the first study demonstrating that a synthetic mixture of bacteria can colonize and persist on lettuce plants, and also showing their synergistic beneficial effect both in the nursery greenhouse as well as the commercial production farm.
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Affiliation(s)
- Santiago A. Vio
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (CONICET/UNLP), Calle 50 227, La Plata 1900, Argentina
| | - María Lina Galar
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (CONICET/UNLP), Calle 50 227, La Plata 1900, Argentina
| | - María Cecilia Gortari
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (CONICET/UNLP), Calle 50 227, La Plata 1900, Argentina
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC-PBA), Calle 526 e/ Calles 10 y 11, La Plata 1900, Argentina
| | - Pedro Balatti
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC-PBA), Calle 526 e/ Calles 10 y 11, La Plata 1900, Argentina
- Centro de Investigaciones de Fitopatología, CIDEFI (CIC–UNLP), Calle 60 y 119, La Plata 1900, Argentina
| | - Mariana Garbi
- Climatología y Fenología Agrícola, Facultad de Ciencias Agrarias y Forestales, UNLP, Calle 60 y 119, La Plata 1900, Argentina
| | - Aníbal Roberto Lodeiro
- Instituto de Biotecnología y Biología Molecular, IBBM (CONICET/UNLP), Calle 47 y 115, La Plata 1900, Argentina
- Genética, Facultad de Ciencias Agrarias y Forestales, UNLP, Calle 60 y 119, La Plata 1900, Argentina
| | - María Flavia Luna
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (CONICET/UNLP), Calle 50 227, La Plata 1900, Argentina
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC-PBA), Calle 526 e/ Calles 10 y 11, La Plata 1900, Argentina
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5
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Lincoln N, Santiago RP, Tatum D, Del Valle-Echevarria AR. Evidence of Downregulation in Atmospheric Nitrogen-Fixation Associated with Native Hawaiian Sugarcane ( Saccharum officinarum L.) Cultivars. PLANTS (BASEL, SWITZERLAND) 2023; 12:605. [PMID: 36771690 PMCID: PMC9920620 DOI: 10.3390/plants12030605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
The study of nitrogen fixation in sugarcane has a long history that has demonstrated high potential but with substantial variation in results. This 32-month study sought to assess the response of nitrogen fixation associated with sugarcane (Saccharum officinarum L. cvs. 'Akoki, Honua'ula, and 'Ula) to available soil nitrogen. Plants were grown in large pots of perlite along with a fixing and a non-fixing plant control and administered liquid fertigation with varying amounts of isotopically enriched nitrogen. Assessment of nitrogen fixation utilized nitrogen isotope tracing and acetylene reduction assay in the target and control plants. Isotope enrichment and acetylene reduction assay both indicated that nitrogen fixation peaked under low nitrogen application, and declined with higher application rates, with agreement between the two methods. These results suggest that sugarcane engages in a downregulation of nitrogen fixation under high nitrogen availability, potentially explaining the high variation in published experimental results. This suggests that nitrogen management and fertilization strategy can impact the atmospheric inputs of nitrogen in sugarcane cultivation, and the potential to improve nitrogen application efficiency in cropping systems utilizing sugarcane.
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Affiliation(s)
- Noa Lincoln
- Tropical Plant and Soil Sciences Department, University of Hawai‘i, Honolulu, HI 96822, USA
| | - Reinier Paul Santiago
- Department of Natural Resources and Environmental Management, University of Hawai‘i, Honolulu, HI 96822, USA
| | - Derek Tatum
- Tropical Plant and Soil Sciences Department, University of Hawai‘i, Honolulu, HI 96822, USA
| | - Angel R. Del Valle-Echevarria
- Hawai‘i Agriculture Research Center, Waipahu, HI 96797, USA
- Agricultural Sector Team, Deep Science Ventures, London EC3 1JP, UK
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6
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He Y, Xie Z, Zhang H, Liebl W, Toyama H, Chen F. Oxidative Fermentation of Acetic Acid Bacteria and Its Products. Front Microbiol 2022; 13:879246. [PMID: 35685922 PMCID: PMC9171043 DOI: 10.3389/fmicb.2022.879246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Acetic acid bacteria (AAB) are a group of Gram-negative, strictly aerobic bacteria, including 19 reported genera until 2021, which are widely found on the surface of flowers and fruits, or in traditionally fermented products. Many AAB strains have the great abilities to incompletely oxidize a large variety of carbohydrates, alcohols and related compounds to the corresponding products mainly including acetic acid, gluconic acid, gulonic acid, galactonic acid, sorbose, dihydroxyacetone and miglitol via the membrane-binding dehydrogenases, which is termed as AAB oxidative fermentation (AOF). Up to now, at least 86 AOF products have been reported in the literatures, but no any monograph or review of them has been published. In this review, at first, we briefly introduce the classification progress of AAB due to the rapid changes of AAB classification in recent years, then systematically describe the enzymes involved in AOF and classify the AOF products. Finally, we summarize the application of molecular biology technologies in AOF researches.
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Affiliation(s)
- Yating He
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhenzhen Xie
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huan Zhang
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wolfgang Liebl
- Department of Microbiology, Technical University of Munich, Freising, Germany
| | - Hirohide Toyama
- Department of Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Okinawa, Japan
| | - Fusheng Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Fusheng Chen
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7
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Dissection and reconstitution provide insights into electron transport in the membrane-bound aldehyde dehydrogenase complex of
Gluconacetobacter diazotrophicus. J Bacteriol 2022; 204:e0055821. [DOI: 10.1128/jb.00558-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acetic acid bacteria catalyze the two-step oxidation of ethanol to acetic acid using the membrane-bound enzymes pyrroloquinoline quinone-dependent alcohol dehydrogenase and molybdopterin-dependent aldehyde dehydrogenase (ALDH). Although the reducing equivalents from the substrate are transferred to ubiquinone in the membrane, intramolecular electron transport in ALDH is not understood. Here, we purified the AldFGH complex, the membrane-bound ALDH that is physiologically relevant to acetic acid fermentation in
Gluconacetobacter diazotrophicus
strain PAL5. The purified AldFGH complex showed acetaldehyde:ubiquinone (Q
2
) oxidoreductase activity.
C
-type cytochromes of the AldFGH complex (in the AldF subunit) were reduced by acetaldehyde. Then, we genetically dissected the AldFGH complex into AldGH and AldF units and reconstituted them. The AldGH subcomplex showed acetaldehyde:ferricyanide oxidoreductase activity, but not Q
2
reductase activity. The ALDH activity of AldGH was not found in membranes but in the soluble fraction of the recombinant strain, suggesting that the AldF subunit is responsible for membrane binding of the AldFGH complex. AldFGH complex reconstituted from the AldGH subcomplex and AldF showed Q
2
reductase activity. Absorption spectra of the purified AldGH subcomplex suggested the presence of an [Fe–S] cluster, which can be reduced by acetaldehyde. We propose a model in which electrons from the substrate are abstracted by a molybdopterin in the AldH subunit and transferred to [Fe–S] cluster(s) in the AldG subunit, followed by electron transport to
c
-type cytochrome centers in the AldF subunit, which is the site of ubiquinone reduction in the membrane.
Importance
Two membrane-bound enzymes of acetic acid bacteria—pyrroloquinoline quinone-dependent alcohol dehydrogenase and molybdopterin-dependent aldehyde dehydrogenase (ALDH)—are responsible for vinegar production. Upon oxidation of acetaldehyde, ALDH reduces ubiquinone in the cytoplasmic membrane. ALDH is an enzyme complex of three subunits. Here, we tried to understand how ALDH works by using a classical biochemical approach and genetic engineering to dissect the enzyme complex into soluble and membrane-bound parts. The soluble part had limited activity
in vitro
, and did not reduce ubiquinone. However, enzyme complex reconstituted from the soluble and membrane-bound parts showed ubiquinone reduction activity. The proposed working model of ALDH provides a better understanding of how the enzyme works in the vinegar fermentation process.
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Yang H, Chen T, Wang M, Zhou J, Liebl W, Barja F, Chen F. Molecular biology: Fantastic toolkits to improve knowledge and application of acetic acid bacteria. Biotechnol Adv 2022; 58:107911. [PMID: 35033586 DOI: 10.1016/j.biotechadv.2022.107911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/27/2021] [Accepted: 01/09/2022] [Indexed: 12/24/2022]
Abstract
Acetic acid bacteria (AAB) are a group of gram-negative, obligate aerobic bacteria within the Acetobacteraceae family of the alphaproteobacteria class, which are distributed in a wide variety of different natural sources that are rich in sugar and alcohols, as well as in several traditionally fermented foods. Their capabilities are not limited to the production of acetic acid and the brewing of vinegar, as their names suggest. They can also fix nitrogen and produce various kinds of aldehydes, ketones and other organic acids by incomplete oxidation (also referred to as oxidative fermentation) of the corresponding alcohols and/or sugars, as well as pigments and exopolysaccharides (EPS). In order to gain more insight into these organisms, molecular biology techniques have been extensively applied in almost all aspects of AAB research, including their identification and classification, acid resistance mechanisms, oxidative fermentation, EPS production, thermotolerance and so on. In this review, we mainly focus on the application of molecular biological technologies in the advancement of research into AAB while presenting the progress of the latest studies using these techniques.
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Affiliation(s)
- Haoran Yang
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Tao Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Min Wang
- State Key Laboratory of Food Nutrition and Safety, College of Biotechnology, Tianjin University of Science &Technology, Tianjin, China
| | - Jingwen Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | | | - François Barja
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Sciences III, Geneva, Switzerland
| | - Fusheng Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China.
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9
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Bellenberg S, Turner S, Seidel L, van Wyk N, Zhang R, Sachpazidou V, Embile RF, Walder I, Leiviskä T, Dopson M. Towards Bioleaching of a Vanadium Containing Magnetite for Metal Recovery. Front Microbiol 2021; 12:693615. [PMID: 34276626 PMCID: PMC8278310 DOI: 10.3389/fmicb.2021.693615] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/24/2021] [Indexed: 01/04/2023] Open
Abstract
Vanadium - a transition metal - is found in the ferrous-ferric mineral, magnetite. Vanadium has many industrial applications, such as in the production of high-strength low-alloy steels, and its increasing global industrial consumption requires new primary sources. Bioleaching is a biotechnological process for microbially catalyzed dissolution of minerals and wastes for metal recovery such as biogenic organic acid dissolution of bauxite residues. In this study, 16S rRNA gene amplicon sequencing was used to identify microorganisms in Nordic mining environments influenced by vanadium containing sources. These data identified gene sequences that aligned to the Gluconobacter genus that produce gluconic acid. Several strategies for magnetite dissolution were tested including oxidative and reductive bioleaching by acidophilic microbes along with dissimilatory reduction by Shewanella spp. that did not yield significant metal release. In addition, abiotic dissolution of the magnetite was tested with gluconic and oxalic acids, and yielded 3.99 and 81.31% iron release as a proxy for vanadium release, respectively. As a proof of principle, leaching via gluconic acid production by Gluconobacter oxydans resulted in a maximum yield of 9.8% of the available iron and 3.3% of the vanadium. Addition of an increased concentration of glucose as electron donor for gluconic acid production alone, or in combination with calcium carbonate to buffer the pH, increased the rate of iron dissolution and final vanadium recoveries. These data suggest a strategy of biogenic organic acid mediated vanadium recovery from magnetite and point the way to testing additional microbial species to optimize the recovery.
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Affiliation(s)
- Sören Bellenberg
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Stephanie Turner
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Laura Seidel
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Nathan van Wyk
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Ruichi Zhang
- Chemical Process Engineering, University of Oulu, Oulu, Finland
| | - Varvara Sachpazidou
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | | | - Ingar Walder
- Kjeøy Research & Education Center, Vestbygd, Norway
| | - Tiina Leiviskä
- Chemical Process Engineering, University of Oulu, Oulu, Finland
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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10
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Fricke PM, Klemm A, Bott M, Polen T. On the way toward regulatable expression systems in acetic acid bacteria: target gene expression and use cases. Appl Microbiol Biotechnol 2021; 105:3423-3456. [PMID: 33856535 PMCID: PMC8102297 DOI: 10.1007/s00253-021-11269-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/24/2021] [Accepted: 04/04/2021] [Indexed: 01/06/2023]
Abstract
Acetic acid bacteria (AAB) are valuable biocatalysts for which there is growing interest in understanding their basics including physiology and biochemistry. This is accompanied by growing demands for metabolic engineering of AAB to take advantage of their properties and to improve their biomanufacturing efficiencies. Controlled expression of target genes is key to fundamental and applied microbiological research. In order to get an overview of expression systems and their applications in AAB, we carried out a comprehensive literature search using the Web of Science Core Collection database. The Acetobacteraceae family currently comprises 49 genera. We found overall 6097 publications related to one or more AAB genera since 1973, when the first successful recombinant DNA experiments in Escherichia coli have been published. The use of plasmids in AAB began in 1985 and till today was reported for only nine out of the 49 AAB genera currently described. We found at least five major expression plasmid lineages and a multitude of further expression plasmids, almost all enabling only constitutive target gene expression. Only recently, two regulatable expression systems became available for AAB, an N-acyl homoserine lactone (AHL)-inducible system for Komagataeibacter rhaeticus and an L-arabinose-inducible system for Gluconobacter oxydans. Thus, after 35 years of constitutive target gene expression in AAB, we now have the first regulatable expression systems for AAB in hand and further regulatable expression systems for AAB can be expected. KEY POINTS: • Literature search revealed developments and usage of expression systems in AAB. • Only recently 2 regulatable plasmid systems became available for only 2 AAB genera. • Further regulatable expression systems for AAB are in sight.
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Affiliation(s)
- Philipp Moritz Fricke
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Angelika Klemm
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Tino Polen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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11
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Daucus carota L. Seed Inoculation with a Consortium of Bacteria Improves Plant Growth, Soil Fertility Status and Microbial Community. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11073274] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The present work aimed to study suitability of a consortium of Azospirillum brasilense, Gluconacetobacter diazotrophicus, Herbaspirillum seropedicae, and Burkholderia ambifaria as biofertilizers. Strains were assayed for plant growth-promoting characteristics (i.e., auxins production, phosphate solubilizing capability, and 1-aminocyclopropane-1-carboxylate deaminase activity). The consortium of four bacteria was then inoculated on carrot seeds and tested in an open field experiment. During the open field experiment, plant growth (morphological parameters, chlorophylls, and carotenoids), soil chemical analysis, and molecular and physiological profiles of soils were investigated. Each strain produced different amounts of indole-3acetic acid and several indole-derivates molecules. All strains showed phosphate solubilization capability, while 1-aminocyclopropane-1-carboxylate deaminase activity was only detected in H. seropedicae and B. ambifaria. The bacterial consortium of the four strains gave interesting results in the open field cultivation of carrot. Plant development was positively affected by the presence of the consortium, as was soil fertility and microbial community structure and diversity. The present work allowed for deepening our knowledge on four bacteria, already known for years for having several interesting characteristics, but whose interactions were almost unknown, particularly in view of their use as a consortium in a valid fertilization strategy, in substitution of agrochemicals for a sustainable agriculture.
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12
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Qiu X, Zhang Y, Hong H. Classification of acetic acid bacteria and their acid resistant mechanism. AMB Express 2021; 11:29. [PMID: 33595734 PMCID: PMC7889782 DOI: 10.1186/s13568-021-01189-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/04/2021] [Indexed: 12/14/2022] Open
Abstract
Acetic acid bacteria (AAB) are obligate aerobic Gram-negative bacteria that are commonly used in vinegar fermentation because of their strong capacity for ethanol oxidation and acetic acid synthesis as well as their acid resistance. However, low biomass and low production rate due to acid stress are still major challenges that must be overcome in industrial processes. Although acid resistance in AAB is important to the production of high acidity vinegar, the acid resistance mechanisms of AAB have yet to be fully elucidated. In this study, we discuss the classification of AAB species and their metabolic processes and review potential acid resistance factors and acid resistance mechanisms in various strains. In addition, we analyze the quorum sensing systems of Komagataeibacter and Gluconacetobacter to provide new ideas for investigation of acid resistance mechanisms in AAB in the form of signaling pathways. The results presented herein will serve as an important reference for selective breeding of high acid resistance AAB and optimization of acetic acid fermentation processes.
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Affiliation(s)
- Xiaoman Qiu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China
- National Engineering Technique Research Center for Biotechnology, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China
| | - Yao Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China
- National Engineering Technique Research Center for Biotechnology, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China
| | - Housheng Hong
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China.
- National Engineering Technique Research Center for Biotechnology, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China.
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13
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Miah R, Nina S, Murate T, Kataoka N, Matsutani M, Matsushita K, Yakushi T. Major aldehyde dehydrogenase AldFGH of Gluconacetobacter diazotrophicus is independent of pyrroloquinoline quinone but dependent on molybdopterin for acetic acid fermentation. Appl Microbiol Biotechnol 2021; 105:2341-2350. [PMID: 33591385 DOI: 10.1007/s00253-021-11144-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/12/2021] [Accepted: 01/26/2021] [Indexed: 11/28/2022]
Abstract
Acetic acid fermentation involves the oxidation of ethanol to acetic acid via acetaldehyde as the intermediate and is catalyzed by the membrane-bound alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) of acetic acid bacteria. Although ADH depends on pyrroloquinoline quinone (PQQ), the prosthetic group associated with ALDH remains a matter of debate. This study aimed to address the dependency of ALDH of Gluconacetobacter diazotrophicus strain PAL5 on PQQ and the physiological role of ALDH in acetic acid fermentation. We constructed deletion mutant strains for both the ALDH gene clusters of PAL5, aldFGH and aldSLC. In addition, the adhAB operon for ADH was eliminated, since it shows ALDH activity. The triple-deletion derivative ΔaldFGH ΔaldSLC ΔadhAB failed to show ALDH activity, which suggested that ALDH activity in PAL5 is derived from these three enzyme complexes. Since the single-gene cluster deletion derivative ΔaldFGH lost most ALDH activity, and accumulated much higher acetaldehyde than wild type under acetic acid fermentation conditions, we concluded that AldFGH functions as the major ALDH in PAL5. Furthermore, deletion of the PQQ biosynthesis gene cluster (pqqABCDE) abolished ADH activity completely, but did not affect ALDH activity. Instead, the molybdopterin biosynthesis gene deletion derivatives lost ALDH activity. Thus, we concluded that the AldFGH and AldSLC complexes of Ga. diazotrophicus PAL5 require a form of molybdopterin but not PQQ for ALDH activity. KEY POINTS: • AldFGH is the major aldehyde dehydrogenase in Gluconacetobacter diazotrophicus PAL5. • Acetaldehyde accumulated from ethanol in the absence of AldFGH. • Molybdopterin, rather than pyrroloquinoline quinone, is required for AldFGH.
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Affiliation(s)
- Roni Miah
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Shun Nina
- Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Takeru Murate
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Naoya Kataoka
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan.,Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Minenosuke Matsutani
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Kazunobu Matsushita
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan.,Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Toshiharu Yakushi
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan. .,Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan. .,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, 753-8515, Japan.
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14
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Sombolestani AS, Cleenwerck I, Cnockaert M, Borremans W, Wieme AD, Moutia Y, Spaepen S, De Vuyst L, Vandamme P. Gluconacetobacter dulcium sp. nov., a novel Gluconacetobacter species from sugar-rich environments. Int J Syst Evol Microbiol 2020; 71. [PMID: 33351739 DOI: 10.1099/ijsem.0.004569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A phylogenomic analysis based on 107 single-copy core genes revealed that three strains from sugar-rich environments, i.e. LMG 1728T, LMG 1731 and LMG 22058, represented a single, novel Gluconacetobacter lineage with Gluconacetobacter liquefaciens as nearest validly named neighbour. OrthoANIu and digital DNA-DNA hybridization analyses among these strains and Gluconacetobacter type strains confirmed that the three strains represented a novel Gluconacetobacter species. Biochemical characteristics and MALDI-TOF mass spectra allowed differentiation of this novel species from the type strains of G. liquefaciens and other closely related Gluconacetobacter species. We therefore propose to classify strains LMG 1728T, LMG 1731 and LMG 22058 in the novel species Gluconacetobacter dulcium sp. nov., with LMG 1728T (=CECT 30142T) as the type strain.
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Affiliation(s)
- Atena Sadat Sombolestani
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Wim Borremans
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Anneleen D Wieme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Yvan Moutia
- Plant Pathology Department, Mauritius Sugarcane Industry Research Institute, Mauritius Cane Industry Authority, 1, Moka Road, Réduit, Mauritius.,Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20 - Box 2460, B-3001 Heverlee, Belgium
| | - Stijn Spaepen
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20 - Box 2460, B-3001 Heverlee, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Peter Vandamme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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15
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Aswini K, Gopal NO, Uthandi S. Optimized culture conditions for bacterial cellulose production by Acetobacter senegalensis MA1. BMC Biotechnol 2020; 20:46. [PMID: 32843009 PMCID: PMC7448454 DOI: 10.1186/s12896-020-00639-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/10/2020] [Indexed: 11/10/2022] Open
Abstract
Background Cellulose, the most versatile biomolecule on earth, is available in large quantities from plants. However, cellulose in plants is accompanied by other polymers like hemicellulose, lignin, and pectin. On the other hand, pure cellulose can be produced by some microorganisms, with the most active producer being Acetobacter xylinum. A. senengalensis is a gram-negative, obligate aerobic, motile coccus, isolated from Mango fruits in Senegal, capable of utilizing a variety of sugars and produce cellulose. Besides, the production is also influenced by other culture conditions. Previously, we isolated and identified A. senengalensis MA1, and characterized the bacterial cellulose (BC) produced. Results The maximum cellulose production by A. senengalensis MA1 was pre-optimized for different parameters like carbon, nitrogen, precursor, polymer additive, pH, temperature, inoculum concentration, and incubation time. Further, the pre-optimized parameters were pooled, and the best combination was analyzed by using Central Composite Design (CCD) of Response Surface Methodology (RSM). Maximum BC production was achieved with glycerol, yeast extract, and PEG 6000 as the best carbon and nitrogen sources, and polymer additive, respectively, at 4.5 pH and an incubation temperature of 33.5 °C. Around 20% of inoculum concentration gave a high yield after 30 days of inoculation. The interactions between culture conditions optimized by CCD included alterations in the composition of the HS medium with 50 mL L− 1 of glycerol, 7.50 g L− 1 of yeast extract at pH 6.0 by incubating at a temperature of 33.5 °C along with 7.76 g L− 1 of PEG 6000. This gave a BC yield of wet weight as 469.83 g L− 1. Conclusion The optimized conditions of growth medium resulted in enhanced production of bacterial cellulose by A. senegalensis MA1, which is around 20 times higher than that produced using an unoptimized HS medium. Further, the cellulose produced can be used in food and pharmaceuticals, for producing high-quality paper, wound dressing material, and nanocomposite films for food packaging.
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Affiliation(s)
- K Aswini
- Biocatalysts Laboratory, Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India
| | - N O Gopal
- Biocatalysts Laboratory, Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India
| | - Sivakumar Uthandi
- Biocatalysts Laboratory, Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India.
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16
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Pellegrini M, Ercole C, Di Zio C, Matteucci F, Pace L, Del Gallo M. In vitro and in planta antagonistic effects of plant growth-promoting rhizobacteria consortium against soilborne plant pathogens of Solanum tuberosum and Solanum lycopersicum. FEMS Microbiol Lett 2020; 367:5860279. [PMID: 32562424 DOI: 10.1093/femsle/fnaa099] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/19/2020] [Indexed: 01/07/2023] Open
Abstract
Potatoes (Solanum tuberosum L.) and tomatoes (Solanum lycopersicum L.), among the main crops belonging to the Solanaceae family, are attacked by several pathogens. Among them Fusarium oxysporum f. sp. radicis-lycopersici and Rhizoctonia solani are very common and cause significant losses. Four plant growth-promoting rhizobacteria, Azospirillum brasilense, Gluconacetobacter diazotrophicus, Herbaspirillum seropedicae and Burkholderia ambifaria were tested against these pathogens. In vitro antagonistic activities of single strains were assessed through dual culture plates. Strains showing antagonistic activity (G. diazotrophicus, H. seropedicae and B. ambifaria) were combined and, after an in vitro confirmation, the consortium was applied on S. lycopersicum and S. tuberosum in a greenhouse pot experiment. The bioprotection was assessed in pre-emergence (infection before germination) and post-emergence (infection after germination). The consortium was able to successfully counteract the infection of both F. oxysporum and R. solani, allowing a regular development of plants. The biocontrol of the fungal pathogens was highlighted both in pre-emergence and post-emergence conditions. This selected consortium could be a valid alternative to agrochemicals and could be exploited as biocontrol agent to counteract losses due to these pathogenic fungi.
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Affiliation(s)
- Marika Pellegrini
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67010 Coppito, L'Aquila, Italy
| | - Claudia Ercole
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67010 Coppito, L'Aquila, Italy
| | - Chiara Di Zio
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67010 Coppito, L'Aquila, Italy
| | - Federica Matteucci
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67010 Coppito, L'Aquila, Italy
| | - Loretta Pace
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67010 Coppito, L'Aquila, Italy
| | - Maddalena Del Gallo
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67010 Coppito, L'Aquila, Italy
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17
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Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
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Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
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18
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Naloka K, Yukphan P, Matsutani M, Matsushita K, Theeragool G. Komagataeibacter diospyri sp. nov., a novel species of thermotolerant bacterial nanocellulose-producing bacterium. Int J Syst Evol Microbiol 2020; 70:251-258. [PMID: 31622229 DOI: 10.1099/ijsem.0.003745] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thermotolerant bacterial nanocellulose-producing strains, designated MSKU 9T and MSKU 15, were isolated from persimmon and sapodilla fruits, respectively. These strains were aerobic, Gram-stain-negative, had rod-shaped cells, were non-motile and formed white-cream colonies. Phylogeny based on the 16S rRNA gene sequences revealed that MSKU 9T and MSKU 15 represented members of the genus Komagataeibacter and formed a monophyletic branch with K. swingsii JCM 17123T and K. europaeus DSM 6160T. The genomic analysis revealed that overall genomic relatedness index values of MSKU 9T with K. swingsii JCM 17123T and K. europaeus DSM 6160T were ~90 % average nucleotide identity (ANI) and ≤58.2 % digital DNA-DNA hybridization (dDDH), respectively. MSKU 9T and MSKU 15 can be differentiated from the closely related K. swingsii JCM 17123T by their growth on 30 % d-glucose and ability to utilize and to form acid from raffinose and sucrose as carbon sources, and from K. europaeus DSM 6160T by their ability to grow without acetic acid. The genomic DNA G+C contents of MSKU 9T and MSKU 15 were 60.4 and 60.2 mol%, respectively. The major fatty acids of MSKU 9T and MSKU 15 were summed feature 8 (C18 : 1 ω7c and/or C18 : 1ω6c). The respiratory quinone was determined to be Q10. On the basis of the results of the polyphasic taxonomic analysis, MSKU 9T (=TBRC 9844T=NBRC 113802T) represents a novel species of the genus Komagataeibacter, for which the name Komagataeibacter diospyri sp. nov. is proposed.
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Affiliation(s)
- Kallayanee Naloka
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Pattaraporn Yukphan
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani 12120, Thailand
| | - Minenosuke Matsutani
- Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Kazunobu Matsushita
- Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8515, Japan.,Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan.,Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Gunjana Theeragool
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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19
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Charreau H, Cavallo E, Foresti ML. Patents involving nanocellulose: Analysis of their evolution since 2010. Carbohydr Polym 2020; 237:116039. [PMID: 32241405 DOI: 10.1016/j.carbpol.2020.116039] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/15/2020] [Accepted: 02/18/2020] [Indexed: 12/15/2022]
Abstract
During the last two decades cellulosic nanomaterials have been the subject of much research around the world. Moreover, in the last few years, increasing industrial interest on the field enabled the setting-up of the first facilities producing commercial quantities of nanocelluloses; whereas a number of inventions involving cellulose nano-objects are claimed every year. In this context, the current article describes the recent evolution (from 2010 till 2017) of published patents which explicitly include in their title, abstract and/or claims references to cellulose nano-objects such as cellulose nanocrystals, cellulose nanofibrils and bacterial nanocellulose. Results evidence the astonishing increase in nanocellulose patents since 2010, and specially within the last three years surveyed (i.e. 2015-2017), when published documents accounted for ca. 70 % of the total number of patents published since 2010. Besides patent timelines, data is analysed in terms of patent owners, countries of application, and citing number.
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Affiliation(s)
- Hernán Charreau
- Área de Inteligencia Tecnológica, Clarke, Modet y Cia. Argentina S.A., Lavalle 190, 3° Piso, Buenos Aires, Argentina; Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
| | - Ema Cavallo
- Grupo de Biotecnología y Materiales Biobasados, Instituto de Tecnología en Polímeros y Nanotecnología (ITPN-UBA-CONICET), Facultad de Ingeniería, Universidad de Buenos Aires, Las Heras 2214 (CP 1127AAR), Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; Departamento de Ingeniería Química, Facultad de Ingeniería, Universidad de Buenos Aires, Av. Intendente Güiraldes 2620 (CP 1428BGA) - Pabellón de Industrias, Ciudad Universitaria, Buenos Aires, Argentina
| | - María Laura Foresti
- Grupo de Biotecnología y Materiales Biobasados, Instituto de Tecnología en Polímeros y Nanotecnología (ITPN-UBA-CONICET), Facultad de Ingeniería, Universidad de Buenos Aires, Las Heras 2214 (CP 1127AAR), Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
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20
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Aranda-Díaz A, Obadia B, Dodge R, Thomsen T, Hallberg ZF, Güvener ZT, Ludington WB, Huang KC. Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance. eLife 2020; 9:51493. [PMID: 31995029 PMCID: PMC7025823 DOI: 10.7554/elife.51493] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/28/2020] [Indexed: 12/11/2022] Open
Abstract
Predicting antibiotic efficacy within microbial communities remains highly challenging. Interspecies interactions can impact antibiotic activity through many mechanisms, including alterations to bacterial physiology. Here, we studied synthetic communities constructed from the core members of the fruit fly gut microbiota. Co-culturing of Lactobacillus plantarum with Acetobacter species altered its tolerance to the transcriptional inhibitor rifampin. By measuring key metabolites and environmental pH, we determined that Acetobacter species counter the acidification driven by L. plantarum production of lactate. Shifts in pH were sufficient to modulate L. plantarum tolerance to rifampin and the translational inhibitor erythromycin. A reduction in lag time exiting stationary phase was linked to L. plantarum tolerance to rifampicin, opposite to a previously identified mode of tolerance to ampicillin in E. coli. This mechanistic understanding of the coupling among interspecies interactions, environmental pH, and antibiotic tolerance enables future predictions of growth and the effects of antibiotics in more complex communities.
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Affiliation(s)
- Andrés Aranda-Díaz
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Benjamin Obadia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Ren Dodge
- Department of Embryology, Carnegie Institution of Washington, Baltimore, United States
| | - Tani Thomsen
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Zachary F Hallberg
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States
| | - Zehra Tüzün Güvener
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - William B Ludington
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Department of Embryology, Carnegie Institution of Washington, Baltimore, United States
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, United States.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States.,Chan Zuckerberg Biohub, San Francisco, United States
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21
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Rodriguez MV, Tano J, Ansaldi N, Carrau A, Srebot MS, Ferreira V, Martínez ML, Cortadi AA, Siri MI, Orellano EG. Anatomical and Biochemical Changes Induced by Gluconacetobacter diazotrophicus Stand Up for Arabidopsis thaliana Seedlings From Ralstonia solanacearum Infection. FRONTIERS IN PLANT SCIENCE 2019; 10:1618. [PMID: 31921261 PMCID: PMC6936193 DOI: 10.3389/fpls.2019.01618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 11/18/2019] [Indexed: 05/09/2023]
Abstract
Nowadays, fertilization and pest control are carried out using chemical compounds that contaminate soil and deteriorate human health. Plant growth promoting bacteria endophytes (PGPBEs), are a well-studied group of bacteria that offers benefits to the host plant, such as phytostimulation, biofertilization, and protection against other microorganisms. The study of Gluconacetobacter diazotrophicus-which belongs to PGPBEs-aids the development of alternative strategies of an integrated approach for crop management practices. Ralstonia solanacearum is responsible for bacterial wilt disease. This phytopathogen is of great interest worldwide due to the enormous economic losses it causes. In this study the action of G. diazotrophicus as a growth promoting bacterium in Arabidopsis thaliana seedlings is analyzed, evaluating the antagonistic mechanisms of this beneficial endophytic bacterium during biotic stress produced by R. solanacearum. Effective colonization of G. diazotrophicus was determined through bacterial counting assays, evaluation of anatomical and growth parameters, and pigments quantification. Biocontrol assays were carried out with Ralstonia pseudosolanacearum GMI1000 model strain and R. solanacearum A21 a recently isolated strain. Inoculation of A. thaliana (Col 0) with G. diazotrophicus Pal 5 triggers a set of biochemical and structural changes in roots, stems, and leaves of seedlings. Discrete callose deposits as papillae were observed at specific sites of root hairs, trichomes, and leaf tissue. Upon R. pseudosolanacearum GMI1000 infection, endophyte-treated plants demonstrated being induced for defense through an augmented callose deposition at root hairs and leaves compared with the non-endophyte-treated controls. The endophytic bacterium appears to be able to prime callose response. Roots and stems cross sections showed that integrity of all tissues was preserved in endophyte-treated plants infected with R. solanacearum A21. The mechanisms of resistance elicited by the plant after inoculation with the endophyte would be greater lignification and sclerosis in tissues and reinforcement of the cell wall through the deposition of callose. As a consequence of this priming in plant defense response, viable phytopathogenic bacteria counting were considerably fewer in endophyte-inoculated plants than in not-inoculated controls. Our results indicate that G. diazotrophicus colonizes A. thaliana plants performing a protective role against the phytopathogenic bacterium R. solanacearum promoting the activation of plant defense system.
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Affiliation(s)
- María V. Rodriguez
- Área Biología Vegetal (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Josefina Tano
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (CONICET-UNR), Universidad Nacional de Rosario, Rosario, Argentina
| | - Nazarena Ansaldi
- Área Biología Vegetal (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Analía Carrau
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (CONICET-UNR), Universidad Nacional de Rosario, Rosario, Argentina
| | - María S. Srebot
- Área Biología Vegetal (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Virginia Ferreira
- Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - María L. Martínez
- Área Biología Vegetal (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Adriana A. Cortadi
- Área Biología Vegetal (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - María I. Siri
- Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Elena G. Orellano
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (CONICET-UNR), Universidad Nacional de Rosario, Rosario, Argentina
- Área Biología Molecular (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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22
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Cvetković D, Ranitović A, Savić D, Joković N, Vidaković A, Pezo L, Markov S. Survival of Wild Strains of Lactobacilli During Kombucha Fermentation and Their Contribution to Functional Characteristics of Beverage. POL J FOOD NUTR SCI 2019. [DOI: 10.31883/pjfns/112276] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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23
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Acetobacter sacchari sp. nov., for a plant growth-promoting acetic acid bacterium isolated in Vietnam. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01497-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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24
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The remarkable three-dimensional network structure of bacterial cellulose for tissue engineering applications. Int J Pharm 2019; 566:631-640. [DOI: 10.1016/j.ijpharm.2019.06.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/21/2019] [Accepted: 06/06/2019] [Indexed: 12/15/2022]
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25
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Lynch KM, Zannini E, Wilkinson S, Daenen L, Arendt EK. Physiology of Acetic Acid Bacteria and Their Role in Vinegar and Fermented Beverages. Compr Rev Food Sci Food Saf 2019; 18:587-625. [DOI: 10.1111/1541-4337.12440] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 02/06/2019] [Accepted: 02/18/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Kieran M. Lynch
- School of Food and Nutritional SciencesUniv. College Cork Cork T12 K8AF Ireland
| | - Emanuele Zannini
- School of Food and Nutritional SciencesUniv. College Cork Cork T12 K8AF Ireland
| | - Stuart Wilkinson
- Global Innovation & Technology CentreAnheuser‐Busch InBev nv/sa Leuven 3000 Belgium
| | - Luk Daenen
- Global Innovation & Technology CentreAnheuser‐Busch InBev nv/sa Leuven 3000 Belgium
| | - Elke K. Arendt
- School of Food and Nutritional SciencesUniv. College Cork Cork T12 K8AF Ireland
- APC Microbiome IrelandUniv. College Cork Cork T12 K8AF Ireland
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26
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Rodrigues AC, Fontão AI, Coelho A, Leal M, Soares da Silva FA, Wan Y, Dourado F, Gama M. Response surface statistical optimization of bacterial nanocellulose fermentation in static culture using a low-cost medium. N Biotechnol 2019; 49:19-27. [DOI: 10.1016/j.nbt.2018.12.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/05/2018] [Accepted: 12/05/2018] [Indexed: 10/27/2022]
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27
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Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:310-319. [PMID: 30550857 PMCID: PMC6364046 DOI: 10.1016/j.gpb.2018.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/11/2018] [Accepted: 06/25/2018] [Indexed: 11/23/2022]
Abstract
We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequence analysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-related species are abundant compared to those in genome-based phylogeny. This phenomenon makes the demarcation of genera within many families ambiguous in the 16S rRNA-based taxonomy. In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes using the CVTree method, which is based on whole-genome information. And many such genera, which are polyphyletic in 16S rRNA-based trees, are well resolved as monophyletic clusters by CVTree. We believe that with genome sequencing of prokaryotes becoming a commonplace, genome-based phylogeny is doomed to play a definitive role in the construction of a natural and objective taxonomy.
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28
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Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol 2018; 35:1547-1549. [PMID: 29722887 DOI: 10.1007/0-387-30745-1_9] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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Affiliation(s)
- Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
- Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Glen Stecher
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Michael Li
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Christina Knyaz
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Koichiro Tamura
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Hachioji, Japan
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
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29
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Dent D. Non-nodular Endophytic Bacterial Symbiosis and the Nitrogen Fixation of Gluconacetobacter diazotrophicus. Symbiosis 2018. [DOI: 10.5772/intechopen.75813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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30
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Laromaine A, Tronser T, Pini I, Parets S, Levkin PA, Roig A. Free-standing three-dimensional hollow bacterial cellulose structures with controlled geometry via patterned superhydrophobic-hydrophilic surfaces. SOFT MATTER 2018; 14:3955-3962. [PMID: 29736513 DOI: 10.1039/c8sm00112j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Bacteria can produce cellulose, one of the most abundant biopolymer on earth, and emerge as an interesting candidate to fabricate advanced materials. Cellulose produced by Komagataeibacter Xylinus, a bacterial strain, is a pure water insoluble biopolymer, without hemicellulose or lignin. Bacterial cellulose (BC) exhibits a nanofibrous porous network microstructure with high strength, low density and high biocompatibility and it has been proposed as cell scaffold and wound healing material. The formation of three dimensional (3D) cellulose self-standing structures is not simple. It either involves complex multi-step synthetic procedures or uses chemical methods to dissolve cellulose and remold it. Here we present an in situ single-step method to produce self-standing 3D-BC structures with controllable wall thickness, size and geometry in a reproducible manner. Parameters such as hydrophobicity of the surfaces, volume of the inoculum and time of culture define the resulting 3D-BC structures. Hollow spheres and convex domes can be easily obtained by changing the surface wettability. The potential of these structures as a 3D cell scaffold is exemplified supporting the growth of mouse embryonic stem cells within a hollow spherical BC structure, indicating its biocompatibility and future prospective.
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Affiliation(s)
- Anna Laromaine
- Institut de Ciència de Materials de Barcelona, Consejo Superior de Investigaciones Científicas (ICMAB-CSIC), Campus de la UAB, 08193 Bellaterra, Catalunya, Spain.
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31
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Gomes RJ, Borges MDF, Rosa MDF, Castro-Gómez RJH, Spinosa WA. Acetic Acid Bacteria in the Food Industry: Systematics, Characteristics and Applications. Food Technol Biotechnol 2018; 56:139-151. [PMID: 30228790 DOI: 10.17113/ftb.56.02.18.5593] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The group of Gram-negative bacteria capable of oxidising ethanol to acetic acid is called acetic acid bacteria (AAB). They are widespread in nature and play an important role in the production of food and beverages, such as vinegar and kombucha. The ability to oxidise ethanol to acetic acid also allows the unwanted growth of AAB in other fermented beverages, such as wine, cider, beer and functional and soft beverages, causing an undesirable sour taste. These bacteria are also used in the production of other metabolic products, for example, gluconic acid, l-sorbose and bacterial cellulose, with potential applications in the food and biomedical industries. The classification of AAB into distinct genera has undergone several modifications over the last years, based on morphological, physiological and genetic characteristics. Therefore, this review focuses on the history of taxonomy, biochemical aspects and methods of isolation, identification and quantification of AAB, mainly related to those with important biotechnological applications.
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Affiliation(s)
- Rodrigo José Gomes
- Department of Food Science and Technology, State University of Londrina, Celso Garcia Cid (PR 445) Road, 86057-970 Londrina, PR, Brazil
| | - Maria de Fatima Borges
- Embrapa Tropical Agroindustry, 2270 Dra. Sara Mesquita Road, 60511-110 Fortaleza, CE, Brazil
| | | | - Raúl Jorge Hernan Castro-Gómez
- Department of Food Science and Technology, State University of Londrina, Celso Garcia Cid (PR 445) Road, 86057-970 Londrina, PR, Brazil
| | - Wilma Aparecida Spinosa
- Department of Food Science and Technology, State University of Londrina, Celso Garcia Cid (PR 445) Road, 86057-970 Londrina, PR, Brazil
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32
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33
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Zhang H, Xu X, Chen X, Yuan F, Sun B, Xu Y, Yang J, Sun D. Complete genome sequence of the cellulose-producing strain Komagataeibacter nataicola RZS01. Sci Rep 2017; 7:4431. [PMID: 28667320 PMCID: PMC5493696 DOI: 10.1038/s41598-017-04589-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/17/2017] [Indexed: 12/29/2022] Open
Abstract
Komagataeibacter nataicola is an acetic acid bacterium (AAB) that can produce abundant bacterial cellulose and tolerate high concentrations of acetic acid. To globally understand its fermentation characteristics, we present a high-quality complete genome sequence of K. nataicola RZS01. The genome consists of a 3,485,191-bp chromosome and 6 plasmids, which encode 3,514 proteins and bear three cellulose synthase operons. Phylogenetic analysis at the genome level provides convincing evidence of the evolutionary position of K. nataicola with respect to related taxa. Genomic comparisons with other AAB revealed that RZS01 shares 36.1%~75.1% of sequence similarity with other AAB. The sequence data was also used for metabolic analysis of biotechnological substrates. Analysis of the resistance to acetic acid at the genomic level indicated a synergistic mechanism responsible for acetic acid tolerance. The genomic data provide a viable platform that can be used to understand and manipulate the phenotype of K. nataicola RZS01 to further improve bacterial cellulose production.
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Affiliation(s)
- Heng Zhang
- Chemicobiology and Functional Materials Institute, Nanjing University of Science and Technology, Nanjing, 210094, China.,School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Xuran Xu
- Chemicobiology and Functional Materials Institute, Nanjing University of Science and Technology, Nanjing, 210094, China.,School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Xiao Chen
- Chemicobiology and Functional Materials Institute, Nanjing University of Science and Technology, Nanjing, 210094, China.,School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Fanshu Yuan
- Chemicobiology and Functional Materials Institute, Nanjing University of Science and Technology, Nanjing, 210094, China.,School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Bianjing Sun
- Chemicobiology and Functional Materials Institute, Nanjing University of Science and Technology, Nanjing, 210094, China.,School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Yunhua Xu
- Department of Life Sciences, Lianyungang Normal College, Lianyungang, 222000, China
| | - Jiazhi Yang
- Chemicobiology and Functional Materials Institute, Nanjing University of Science and Technology, Nanjing, 210094, China. .,School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Dongping Sun
- Chemicobiology and Functional Materials Institute, Nanjing University of Science and Technology, Nanjing, 210094, China. .,School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
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34
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Puri A, Padda KP, Chanway CP. Plant Growth Promotion by Endophytic Bacteria in Nonnative Crop Hosts. ENDOPHYTES: CROP PRODUCTIVITY AND PROTECTION 2017. [DOI: 10.1007/978-3-319-66544-3_2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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35
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Longin C, Guilloux-Benatier M, Alexandre H. Design and Performance Testing of a DNA Extraction Assay for Sensitive and Reliable Quantification of Acetic Acid Bacteria Directly in Red Wine Using Real Time PCR. Front Microbiol 2016; 7:831. [PMID: 27313572 PMCID: PMC4887704 DOI: 10.3389/fmicb.2016.00831] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/17/2016] [Indexed: 11/28/2022] Open
Abstract
Although strategies exist to prevent AAB contamination, the increased interest for wines with low sulfite addition leads to greater AAB spoilage. Hence, there is a real need for a rapid, specific, sensitive, and reliable method for detecting these spoilage bacteria. All these requirements are met by real time Polymerase Chain Reaction (or quantitative PCR; qPCR). Here, we compare existing methods of isolating DNA and their adaptation to a red wine matrix. Two different protocols for isolating DNA and three PCR mix compositions were tested to select the best method. The addition of insoluble polyvinylpolypyrrolidone (PVPP) at 1% (v/v) during DNA extraction using a protocol succeeded in eliminating PCR inhibitors from red wine. We developed a bacterial internal control which was efficient in avoiding false negative results due to decreases in the efficiency of DNA isolation and/or amplification. The specificity, linearity, repeatability, and reproducibility of the method were evaluated. A standard curve was established for the enumeration of AAB inoculated into red wines. The limit of quantification in red wine was 3.7 log AAB/mL and about 2.8 log AAB/mL when the volume of the samples was increased from 1 to 10 mL. Thus, the DNA extraction method developed in this paper allows sensitive and reliable AAB quantification without underestimation thanks to the presence of an internal control. Moreover, monitoring of both the AAB population and the amount of acetic acid in ethanol medium and red wine highlighted that a minimum about 6.0 log cells/mL of AAB is needed to significantly increase the production of acetic acid leading to spoilage.
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Affiliation(s)
- Cédric Longin
- Equipe VAlMiS (Vin, Aliment, Microbiologie, Stress), Institut Universitaire de la Vigne et du Vin Jules Guyot, UMR Procédés Alimentaires et Microbiologiques, AgroSup Dijon - Université de Bourgogne Dijon, France
| | - Michèle Guilloux-Benatier
- Equipe VAlMiS (Vin, Aliment, Microbiologie, Stress), Institut Universitaire de la Vigne et du Vin Jules Guyot, UMR Procédés Alimentaires et Microbiologiques, AgroSup Dijon - Université de Bourgogne Dijon, France
| | - Hervé Alexandre
- Equipe VAlMiS (Vin, Aliment, Microbiologie, Stress), Institut Universitaire de la Vigne et du Vin Jules Guyot, UMR Procédés Alimentaires et Microbiologiques, AgroSup Dijon - Université de Bourgogne Dijon, France
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36
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O'Neill H, Shah R, Evans BR, He J, Pingali SV, Chundawat SPS, Jones AD, Langan P, Davison BH, Urban V. Production of bacterial cellulose with controlled deuterium-hydrogen substitution for neutron scattering studies. Methods Enzymol 2015; 565:123-46. [PMID: 26577730 DOI: 10.1016/bs.mie.2015.08.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Isotopic enrichment of biomacromolecules is a widely used technique that enables the investigation of the structural and dynamic properties to provide information not accessible with natural abundance isotopic composition. This study reports an approach for deuterium incorporation into bacterial cellulose. A media formulation for growth of Acetobacter xylinus subsp. sucrofermentans and Gluconacetobacter hansenii was formulated that supports cellulose production in deuterium (D) oxide. The level of D incorporation can be varied by altering the ratio of deuterated and protiated glycerol used during cell growth in the D2O-based growth medium. Spectroscopic analysis and mass spectrometry show that the level of deuterium incorporation is high (>90%) for the perdeuterated form of bacterial cellulose. The small-angle neutron scattering profiles of the cellulose with different amounts of D incorporation are all similar indicating that there are no structural changes in the cellulose due to substitution of deuterium for hydrogen. In addition, by varying the amount of deuterated glycerol in the media it was possible to vary the scattering length density of the deuterated cellulose. The ability to control deuterium content of cellulose extends the range of experiments using techniques such as neutron scattering to reveal information about the structure and dynamics of cellulose, and its interactions with other biomacromolecules as well as synthetic polymers used for development of composite materials.
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Affiliation(s)
- Hugh O'Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
| | - Riddhi Shah
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA; Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
| | - Barbara R Evans
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Junhong He
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Sai Venkatesh Pingali
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Shishir P S Chundawat
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA; Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Paul Langan
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Brian H Davison
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Volker Urban
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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37
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Reis VM, Teixeira KRDS. Nitrogen fixing bacteria in the family Acetobacteraceae and their role in agriculture. J Basic Microbiol 2015; 55:931-49. [PMID: 25736602 PMCID: PMC7166518 DOI: 10.1002/jobm.201400898] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 01/27/2015] [Indexed: 11/17/2022]
Abstract
For centuries, the Acetobacteraceae is known as a family that harbors many species of organisms of biotechnological importance for industry. Nonetheless, since 1988 representatives of this family have also been described as nitrogen fixing bacteria able to plant growth promotion by a variety of mechanisms. Nitrogen fixation is a biological process that guarantees that the atmospheric N2 is incorporated into organic matter by several bacterial groups. Most representatives of this group, also known as diazotrophic, are generally associated with soil rhizosphere of many plants and also establishing a more specific association living inside roots, leaves, and others plants tissues as endophyte. Their roles as plant growth-promoting microorganisms are generally related to increase in plant biomass, phosphate and other mineral solubilization, and plant pathogen control. Here, we report many of these plant growth-promoting processes related to nitrogen fixing species already described in Acetobacteraceae family, especially Gluconacetobacter diazotrophicus and their importance to agriculture. In addition, a brief review of the state of art of the phylogenetics, main physiological and biochemical characteristics, molecular and functional genomic data of this group of Acetobacteraceae is presented.
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38
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Yetiman AE, Kesmen Z. Identification of acetic acid bacteria in traditionally produced vinegar and mother of vinegar by using different molecular techniques. Int J Food Microbiol 2015; 204:9-16. [PMID: 25828705 DOI: 10.1016/j.ijfoodmicro.2015.03.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 02/24/2015] [Accepted: 03/12/2015] [Indexed: 11/16/2022]
Abstract
Culture-dependent and culture-independent methods were combined for the investigation of acetic acid bacteria (AAB) populations in traditionally produced vinegars and mother of vinegar samples obtained from apple and grape. The culture-independent denaturing gradient gel electrophoresis (DGGE) analysis, which targeted the V7-V8 regions of the 16S rRNA gene, showed that Komagataeibacter hansenii and Komagataeibacter europaeus/Komagataeibacter xylinus were the most dominant species in almost all of the samples analyzed directly. The culture-independent GTG5-rep PCR fingerprinting was used in the preliminary characterization of AAB isolates and species-level identification was carried out by sequencing of the 16S rRNA gene, 16S-23S rDNA internally transcribed to the spacer (ITS) region and tuf gene. Acetobacter okinawensis was frequently isolated from samples obtained from apple while K. europaeus was identified as the dominant species, followed by Acetobacter indonesiensis in the samples originating from grape. In addition to common molecular techniques, real-time PCR intercalating dye assays, including DNA melting temperature (Tm) and high resolution melting analysis (HRM), were applied to acetic acid bacterial isolates for the first time. The target sequence of ITS region generated species-specific HRM profiles and Tm values allowed discrimination at species level.
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Affiliation(s)
- Ahmet E Yetiman
- Erciyes University, Faculty of Engineering, Food Engineering Department, Kayseri, Turkey
| | - Zülal Kesmen
- Erciyes University, Faculty of Engineering, Food Engineering Department, Kayseri, Turkey.
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The oxidative fermentation of ethanol in Gluconacetobacter diazotrophicus is a two-step pathway catalyzed by a single enzyme: alcohol-aldehyde Dehydrogenase (ADHa). Int J Mol Sci 2015; 16:1293-311. [PMID: 25574602 PMCID: PMC4307304 DOI: 10.3390/ijms16011293] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/15/2014] [Indexed: 11/16/2022] Open
Abstract
Gluconacetobacter diazotrophicus is a N2-fixing bacterium endophyte from sugar cane. The oxidation of ethanol to acetic acid of this organism takes place in the periplasmic space, and this reaction is catalyzed by two membrane-bound enzymes complexes: the alcohol dehydrogenase (ADH) and the aldehyde dehydrogenase (ALDH). We present strong evidence showing that the well-known membrane-bound Alcohol dehydrogenase (ADHa) of Ga. diazotrophicus is indeed a double function enzyme, which is able to use primary alcohols (C2-C6) and its respective aldehydes as alternate substrates. Moreover, the enzyme utilizes ethanol as a substrate in a reaction mechanism where this is subjected to a two-step oxidation process to produce acetic acid without releasing the acetaldehyde intermediary to the media. Moreover, we propose a mechanism that, under physiological conditions, might permit a massive conversion of ethanol to acetic acid, as usually occurs in the acetic acid bacteria, but without the transient accumulation of the highly toxic acetaldehyde.
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Trček J, Barja F. Updates on quick identification of acetic acid bacteria with a focus on the 16S-23S rRNA gene internal transcribed spacer and the analysis of cell proteins by MALDI-TOF mass spectrometry. Int J Food Microbiol 2014; 196:137-44. [PMID: 25589227 DOI: 10.1016/j.ijfoodmicro.2014.12.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 11/13/2014] [Accepted: 12/05/2014] [Indexed: 10/24/2022]
Abstract
Acetic acid bacteria have attracted much attention over the past few years, due mainly to their metabolic traits that are of interest to the biotechnology industry. In addition, it turns out that their ecological habitats are almost unlimited since they have been found as symbionts in different insects and also as emerging opportunistic human pathogens. Very surprising is the finding that they colonize niches considered anaerobic, disproving the generalized statement that they are strict aerobes. Since they have taken on different biological roles in our environment, more and more people are charged with the task of identifying them. However, this turns out to be not always easy, especially if we are using phenotypic approaches for identification. A substantial step forward in making the identification of acetic acid bacteria easier was made possible using molecular biological methods, which have been extensively tested since 2000. However, some molecular methods require expensive machines and experienced staff, and moreover the level of their discrimination varies. All these factors must be considered when selecting the most appropriate approach for identifying acetic acid bacteria. With this objective in mind, this review article discusses the benefits and drawbacks of molecular biological methods for identification of acetic acid bacteria, with a focus on the 16S-23S rRNA gene ITS regions and the recently described alternative method for identification of acetic acid bacteria, MALDI-TOF MS.
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Affiliation(s)
- Janja Trček
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, Maribor, Slovenia; Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia.
| | - François Barja
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Jussy-Geneva, Switzerland
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Wang Y, Ji B, Wu W, Wang R, Yang Z, Zhang D, Tian W. Hepatoprotective effects of kombucha tea: identification of functional strains and quantification of functional components. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2014; 94:265-272. [PMID: 23716136 DOI: 10.1002/jsfa.6245] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 05/28/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND Kombucha tea (KT), a traditional health beverage containing potential hepatoprotective agents, is fermented from sugared tea by a symbiotic culture of yeast and bacteria for 8 days. However, the functional strains that produce components for the hepatoprotective property of KT remain unclear. Multiple strains are involved in traditional KT production. Therefore, KT has not been standardized or produced commercially. This study aimed to identify the functional strains and quantify the functional components with hepatoprotective effects in kombucha tea. RESULTS Gluconacetobacter sp. A4 was one of the microorganisms in KT in which the D-saccharic acid-1,4-lactone (DSL) produced by G. sp. A4 was significantly higher than that produced by original tea fungus at 8 days of fermentation. Traditional KT (TKT, tea broth fermented by mixed tea fungus), modified KT (MKT, fermented by single G. sp. A4), and DSL significantly inhibited the acetaminophen-induced increase of alanine aminotransferase, alkaline phosphatase, triglyceride and malondialdehyde, as well as facilitating the reduction of total antioxidant capacity in mice. Furthermore, MKT and TKT are both similar to DSL in terms of protection against acetaminophen-induced liver injury in mice. These results suggested a positive relationship between DSL content and the hepatoprotective effect of TKT, MKT and DSL groups. CONCLUSION G. sp. A4 was concluded to be a potential functional strain and DSL might be the key functional component for the hepatoprotective property in KT. The stronger capability of G. sp. A4 in producing DSL makes it a better choice for the commercial production of KT.
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Affiliation(s)
- Yong Wang
- College of Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
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Acetic acid bacteria and the production and quality of wine vinegar. ScientificWorldJournal 2014; 2014:394671. [PMID: 24574887 PMCID: PMC3918346 DOI: 10.1155/2014/394671] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 11/11/2013] [Indexed: 11/18/2022] Open
Abstract
The production of vinegar depends on an oxidation process that is mainly performed by acetic acid bacteria. Despite the different methods of vinegar production (more or less designated as either “fast” or “traditional”), the use of pure starter cultures remains far from being a reality. Uncontrolled mixed cultures are normally used, but this review proposes the use of controlled mixed cultures. The acetic acid bacteria species determine the quality of vinegar, although the final quality is a combined result of technological process, wood contact, and aging. This discussion centers on wine vinegar and evaluates the effects of these different processes on its chemical and sensory properties.
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Marsh AJ, O'Sullivan O, Hill C, Ross RP, Cotter PD. Sequence-based analysis of the bacterial and fungal compositions of multiple kombucha (tea fungus) samples. Food Microbiol 2013; 38:171-8. [PMID: 24290641 DOI: 10.1016/j.fm.2013.09.003] [Citation(s) in RCA: 182] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 09/03/2013] [Accepted: 09/11/2013] [Indexed: 11/17/2022]
Abstract
Kombucha is a sweetened tea beverage that, as a consequence of fermentation, contains ethanol, carbon dioxide, a high concentration of acid (gluconic, acetic and lactic) as well as a number of other metabolites and is thought to contain a number of health-promoting components. The sucrose-tea solution is fermented by a symbiosis of bacteria and yeast embedded within a cellulosic pellicle, which forms a floating mat in the tea, and generates a new layer with each successful fermentation. The specific identity of the microbial populations present has been the focus of attention but, to date, the majority of studies have relied on culture-based analyses. To gain a more comprehensive insight into the kombucha microbiota we have carried out the first culture-independent, high-throughput sequencing analysis of the bacterial and fungal populations of 5 distinct pellicles as well as the resultant fermented kombucha at two time points. Following the analysis it was established that the major bacterial genus present was Gluconacetobacter, present at >85% in most samples, with only trace populations of Acetobacter detected (<2%). A prominent Lactobacillus population was also identified (up to 30%), with a number of sub-dominant genera, not previously associated with kombucha, also being revealed. The yeast populations were found to be dominated by Zygosaccharomyces at >95% in the fermented beverage, with a greater fungal diversity present in the cellulosic pellicle, including numerous species not identified in kombucha previously. Ultimately, this study represents the most accurate description of the microbiology of kombucha to date.
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Affiliation(s)
- Alan J Marsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; Alimentary Pharmabiotic Centre, University College Cork, Co. Cork, Ireland; Microbiology Department, University College Cork, Co. Cork, Ireland
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Importance of codB for new codA-based markerless gene deletion in Gluconobacter strains. Appl Microbiol Biotechnol 2013; 97:8341-9. [DOI: 10.1007/s00253-013-5164-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 07/26/2013] [Accepted: 07/29/2013] [Indexed: 10/26/2022]
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Illeghems K, De Vuyst L, Weckx S. Complete genome sequence and comparative analysis of Acetobacter pasteurianus 386B, a strain well-adapted to the cocoa bean fermentation ecosystem. BMC Genomics 2013; 14:526. [PMID: 23902333 PMCID: PMC3751514 DOI: 10.1186/1471-2164-14-526] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 07/27/2013] [Indexed: 01/21/2023] Open
Abstract
Background Acetobacter pasteurianus 386B, an acetic acid bacterium originating from a spontaneous cocoa bean heap fermentation, proved to be an ideal functional starter culture for coca bean fermentations. It is able to dominate the fermentation process, thereby resisting high acetic acid concentrations and temperatures. However, the molecular mechanisms underlying its metabolic capabilities and niche adaptations are unknown. In this study, whole-genome sequencing and comparative genome analysis was used to investigate this strain’s mechanisms to dominate the cocoa bean fermentation process. Results The genome sequence of A. pasteurianus 386B is composed of a 2.8-Mb chromosome and seven plasmids. The annotation of 2875 protein-coding sequences revealed important characteristics, including several metabolic pathways, the occurrence of strain-specific genes such as an endopolygalacturonase, and the presence of mechanisms involved in tolerance towards various stress conditions. Furthermore, the low number of transposases in the genome and the absence of complete phage genomes indicate that this strain might be more genetically stable compared with other A. pasteurianus strains, which is an important advantage for the use of this strain as a functional starter culture. Comparative genome analysis with other members of the Acetobacteraceae confirmed the functional properties of A. pasteurianus 386B, such as its thermotolerant nature and unique genetic composition. Conclusions Genome analysis of A. pasteurianus 386B provided detailed insights into the underlying mechanisms of its metabolic features, niche adaptations, and tolerance towards stress conditions. Combination of these data with previous experimental knowledge enabled an integrated, global overview of the functional characteristics of this strain. This knowledge will enable improved fermentation strategies and selection of appropriate acetic acid bacteria strains as functional starter culture for cocoa bean fermentation processes.
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Affiliation(s)
- Koen Illeghems
- Research Group of Industrial Microbiology and Food Biotechnology, IMDO, Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium.
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Nishijima M, Tazato N, Handa Y, Tomita J, Kigawa R, Sano C, Sugiyama J. Gluconacetobacter tumulisoli sp. nov., Gluconacetobacter takamatsuzukensis sp. nov. and Gluconacetobacter aggeris sp. nov., isolated from Takamatsuzuka Tumulus samples before and during the dismantling work in 2007. Int J Syst Evol Microbiol 2013; 63:3981-3988. [PMID: 23793855 DOI: 10.1099/ijs.0.051292-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ten strains of Gram-stain-negative, rod-shaped, non-spore-forming bacteria were isolated from the burial mound soil collected before the dismantling and samples collected during the dismantling work on the Takamatsuzuka Tumulus in Asuka village, Nara Prefecture, Japan in 2007. On the basis of the 16S rRNA gene sequence analysis of the isolates, they were accommodated in the genus Gluconacetobacter (class Alphaproteobacteria) and can be separated into four groups within the cluster containing the genus Gluconacetobacter. One of the groups demonstrated a phylogenetic position identical to that of Gluconacetobacter asukensis, which was isolated from small holes on plaster walls of the stone chamber interior of Kitora Tumulus in Asuka village, Nara Prefecture, Japan. The remaining three groups consisted of novel lineages within the genus Gluconacetobacter. A total of four isolates were selected from each group and carefully identified using a polyphasic approach. The isolates were characterized on the basis of their possessing Q-10 as the major ubiquinone system and C18 : 1ω7c (58.5-65.2 %) as the predominant fatty acid. A DNA-DNA hybridization test was used to determine that the three lineages represented novel species, for which the names Gluconacetobacter tumulisoli sp. nov., Gluconacetobacter takamatsuzukensis sp. nov. and Gluconacetobacter aggeris sp. nov. are proposed. The type strains are T611xx-1-4a(T) ( = JCM 19097(T) = NCIMB 14861(T)), T61213-20-1a(T) ( = JCM 19094(T) = NCIMB 14859(T)) and T6203-4-1a(T) ( = JCM 19092(T) = NCIMB 14860(T)), respectively.
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Affiliation(s)
- Miyuki Nishijima
- Technical Department, TechnoSuruga Laboratory Co. Ltd, 330 Nagasaki, Shimizu-ku, Shizuoka-shi, Shizuoka 424-0065, Japan
| | - Nozomi Tazato
- Technical Department, TechnoSuruga Laboratory Co. Ltd, 330 Nagasaki, Shimizu-ku, Shizuoka-shi, Shizuoka 424-0065, Japan
| | - Yutaka Handa
- Technical Department, TechnoSuruga Laboratory Co. Ltd, 330 Nagasaki, Shimizu-ku, Shizuoka-shi, Shizuoka 424-0065, Japan
| | - Junko Tomita
- Technical Department, TechnoSuruga Laboratory Co. Ltd, 330 Nagasaki, Shimizu-ku, Shizuoka-shi, Shizuoka 424-0065, Japan
| | - Rika Kigawa
- Independent Administrative Institution, National Research Institute for Cultural Properties, Tokyo, 13-43 Ueno-Koen, Taito-ku, Tokyo 110-8713, Japan
| | - Chie Sano
- Independent Administrative Institution, National Research Institute for Cultural Properties, Tokyo, 13-43 Ueno-Koen, Taito-ku, Tokyo 110-8713, Japan
| | - Junta Sugiyama
- TechnoSuruga Laboratory Co., Ltd, Chiba Branch Office & Lab, No. 4 Sanko Building, Room 201, 3-1532-13 Hasama-cho, Funabashi-shi, Chiba 274-0822, Japan
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The effect of deuteration on the structure of bacterial cellulose. Carbohydr Res 2013; 374:82-8. [DOI: 10.1016/j.carres.2013.04.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 04/09/2013] [Accepted: 04/10/2013] [Indexed: 11/19/2022]
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Rapid identification of acetic acid bacteria using MALDI-TOF mass spectrometry fingerprinting. Syst Appl Microbiol 2013. [DOI: 10.1016/j.syapm.2012.09.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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In vitro and in vivo inoculation of four endophytic bacteria on Lycopersicon esculentum. N Biotechnol 2013; 30:666-74. [PMID: 23352842 DOI: 10.1016/j.nbt.2013.01.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 12/21/2012] [Accepted: 01/11/2013] [Indexed: 11/20/2022]
Abstract
Four bacteria selected on the basis of their capability of fixing atmospheric nitrogen, stimulating plant-growth, and protecting the host plant from pathogens - Azospirillum brasilense, Gluconacetobacter diazotrophicus, Herbaspirillum seropedicae, Burkholderia ambifaria - were inoculated on tomato seeds either singularly, in couple and in a four bacteria mixer. Aim of this research was to evaluate: (1) effect of single and mixed cultures on the inoculated plant - plant growth, dry weight, root length and surface, number of leaves, among others; (2) colonization and interactions of the bacteria inside the host plant; (3) localization inside the host of single bacterial strains marked with the gusA reporter gene. The results obtained indicate that all selected microbial strains have colonized Lycopersicon esculentum but in a different way, depending on the single species. A. brasilense, G. diazotrophicus inoculated in vitro singularly and together were the best plant colonizers. In vivo essays, instead, B. ambifaria and the four-bacteria mixer gave the best results. It was possible to localize both A. brasilense and H. seropedicae inside the plant by the gusA reporter gene. The bacterial strains occur along the root axis from the apical zone until to the basal stem, on the shoot from the base up to the leaves. The four bacteria actively colonize tomato seeds and establish an endophytic community inside the plant. This review gives new information about colonization processes, in particular how bacteria interact with plants and whether they are likely to establish themselves in the plant environment after field application as biofertilizers or biocontrol agents.
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Momose A, Ohtake N, Sueyoshi K, Sato T, Nakanishi Y, Akao S, Ohyama T. Nitrogen Fixation and Translocation in Young Sugarcane (Saccharum officinarum L.) Plants Associated with Endophytic Nitrogen-Fixing Bacteria. Microbes Environ 2012; 24:224-30. [PMID: 21566377 DOI: 10.1264/jsme2.me09105] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The tracer (15)N(2) was used to investigate sites of N(2) fixation and the possible translocation of the fixed N. Young sugarcane plants (Saccharum officinarum L.) from a stem cutting were exposed to (15)N(2)-labeled air in a 500 mL plastic cylinder. Plants fed (15)N(2) for 7 days were grown in normal air for a further chase period. After 21 days, about half of the N originating in the stem cutting had been transported to the shoot and roots, suggesting that the cutting played a role in supplying N for growth. After 3 days of feeding, the percentage of N derived from (15)N(2) was higher in the roots (2.22%) and stem cutting (0.271%) than the shoot (0.027%). Most of the fixed N was distributed in the 80% ethanol-insoluble fractions in each plant part, and the (15)N fixed either in the roots or in the stem cutting remained there and was not appreciably transported to the shoot. The results were quite different from the fate of fixed N in soybean nodules, which is rapidly transported from nodules to roots and shoots.
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Affiliation(s)
- Atsushi Momose
- Graduate School of Science and Technology, Niigata University
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