DOCSLIB.ORG

Scope of the Thesis

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Scope of the Thesis Unraveling predatory-prey interactions between bacteria Dissertation To Fulfill the Requirements for the Degree of „Doctor rerum naturalium“ (Dr. rer. nat.) Submitted to the Council of the Faculty of Biology and Pharmacy of the Friedrich Schiller University Jena By Ivana Seccareccia (M.Sc. in Biology) born on 8th April 1986 in Rijeka, Croatia Die Forschungsarbeit im Rahmen dieser Dissertation wurde am Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e.V. – Hans-Knöll–Institut in der Nachwuchsgruppe Sekundärmetabolismus räuberischer Bakterien unter der Betreuung von Dr. habil. Markus Nett von Oktober 2011 bis Oktober 2015 in Jena durchgeführt. Gutachter: ……………………………………………. ………………………………………….… ……………………………………………. Tag der öffentlichen Verteidigung: We make our world significant by the courage of our questions and by the depth of our answers. Carl Sagan Table of Contents 1 Introduction ......................................................................................................................... 6 1.1 Predation in the microbial community ........................................................................... 6 1.2 Bacterial predators .......................................................................................................... 7 1.3 Phases of predation ......................................................................................................... 8 1.3.1 Seeking prey ......................................................................................................... 9 1.3.2 Prey recognition ................................................................................................. 10 1.3.3 Prey killing and consumption ............................................................................. 10 1.4 Bacterial defense against predators .............................................................................. 11 1.4.1 Production of secondary metabolites ................................................................. 11 1.4.2 Morphological adaptations, multicellular structures and high motility ............. 12 1.4.3 Induction of bacterial defense mechanisms ....................................................... 13 1.5 Predation strategies ....................................................................................................... 13 1.5.1 Individual predation ........................................................................................... 14 1.5.2 Group predation .................................................................................................. 14 1.6 The genus Lysobacter ................................................................................................... 15 1.6.1 Predatory behavior of Lysobacter spp. ............................................................... 15 1.7 The genus Cupriavidus ................................................................................................. 16 1.7.1 Predatory behavior of Cupriavidus necator N-1 ................................................ 17 2 Scope of the thesis ............................................................................................................ 19 3 Overview of Manuscripts .................................................................................................. 20 3.1 Manuscripts resulting from the main research project ................................................. 20 3.1.1 Manuscript A ...................................................................................................... 20 3.1.2 Manuscript B ...................................................................................................... 20 3.1.3 Manuscript C ...................................................................................................... 21 3.2 Manuscripts from side projects .................................................................................... 21 3.2.1 Manuscript D ...................................................................................................... 21 3.2.2 Manuscript E ...................................................................................................... 22 4 Published Results .............................................................................................................. 23 4.1 Manuscript A: Quantitative analysis of Lysobacter predation ..................................... 23 4.2 Manuscript B: Unraveling the predator-prey relationship of Cupriavidus necator and Bacillus subtilis ..................................................................................................................... 41 4.3 Manuscript C: Identification of new metallothioneins in the bacterium Cupriavidus necator N-1. .......................................................................................................................... 68 5 Unpublished Results ......................................................................................................... 93 5.1 Evaluation of predatory potential in Cupriavidus spp. ................................................. 93 5.2 Antimicrobial activity of recombinant peptides from C. necator N-1 ......................... 97 6 Discussion ......................................................................................................................... 99 6.1 Analysis of bacterial predation in the laboratory ......................................................... 99 6.2 Comparative analysis of predation behavior among bacteria ..................................... 101 6.2.1 Bacterial predation efficiency across different assays ..................................... 102 6.2.2 Predator-prey ratio and cell contact ................................................................. 104 6.3 Secondary metabolites of C. necator .......................................................................... 105 6.4 Prey-specific factors that influence predation ............................................................ 106 6.5 Distinguishing predation from competition ................................................................ 107 7 Summary ......................................................................................................................... 109 8 Zusammenfassung ........................................................................................................... 111 9 Manuscripts from side projects ....................................................................................... 113 9.1 Manuscript D: Micromonospora schwarzwaldensis sp. nov., a producer of telomycin, isolated from soil. ............................................................................................................... 113 9.2 Manuscript E: Variochelins, lipopeptide siderophores from Variovorax boronicumulans discovered by genome mining. ................................................................ 131 10 List of abbreviations ................................................................................................... 174 11 References .................................................................................................................. 175 12 Acknowledgement ...................................................................................................... 182 13 Eigenständigkeitserklärung ........................................................................................ 184 14 Curriculum Vitae ........................................................................................................ 185 Introduction 1 Introduction 1.1 Predation in the microbial community Microorganisms are living in dynamic and complex communities, communicating and interacting with each other. Microbial interactions can be neutral, beneficial or harmful for the partners involved. Although extensive research is conducted in the field of microbial relationships, it was focused only on few of many different modes of interactions described [1]. When it comes to predation among bacteria, our knowledge is limited and many questions remain to be answered. Predation is considered an important force that shapes microbial communities [2] by simultaneously enforcing selection escape strategies in prey and killing efficiency of predators [3, 4]. Additionally, the ecological role of predators is reflected on the determination of the structure and dynamics in the microbial community. Predation can maintain diversity in the community, as abundant species are statistically more likely to be attacked by predators [5, 6]. Predation is a significant force in trophic interactions between microorganisms that promotes primary production of organic compounds through the process of photosynthesis and chemosynthesis [7]. In aquatic environments, predation pressure leads to more efficient nutrient regeneration and cycling of organic compounds and other nutrients in particular nitrogen and phosphorus [8, 9]. Additionally, predators facilitate release of photosynthetically fixed organic carbon by preying on phytoplankton [10]. Despite the fact that the highest predation pressure comes from microfaunal predators consisting of bacteriovorous protozoa and nematodes [10] bacterial predators have an important role in the microbial food chain, and thus are in the focus of this study. Because of their production of extracellular lytic enzymes, predatory bacteria were already used as biocontrol agents to prevent cyanobacterial blooms in lakes, e.g. Bdellovibrio-like bacteria [11] and Myxococcus sp. [12, 13]. Additionally, the powerful lytic
Load more

Recommended publications
  • Metabolic Engineering of Cupriavidus Necator for Heterotrophic and Autotrophic Alka(E)Ne Production Lucie Crepin, Eric Lombard, Stéphane Guillouet
    Metabolic engineering of Cupriavidus necator for heterotrophic and autotrophic alka(e)ne production Lucie Crepin, Eric Lombard, Stéphane Guillouet To cite this version: Lucie Crepin, Eric Lombard, Stéphane Guillouet. Metabolic engineering of Cupriavidus necator for heterotrophic and autotrophic alka(e)ne production. Metabolic Engineering, Elsevier, 2016, 37, pp.92- 101. 10.1016/j.ymben.2016.05.002. hal-01886395 HAL Id: hal-01886395 https://hal.archives-ouvertes.fr/hal-01886395 Submitted on 14 Apr 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Metabolic Engineering 37 (2016) 92–101 Contents lists available at ScienceDirect Metabolic Engineering journal homepage: www.elsevier.com/locate/ymben Metabolic engineering of Cupriavidus necator for heterotrophic and autotrophic alka(e)ne production Lucie Crépin, Eric Lombard, Stéphane E Guillouet n LISBP, Université de Toulouse, CNRS, INRA, INSA, 135 Avenue de Rangueil, 31077 Toulouse CEDEX 04, France article info abstract Article history: Alkanes of defined carbon chain lengths can serve as alternatives to petroleum-based fuels. Recently, Received 18 March 2016 microbial pathways of alkane biosynthesis have been identified and enabled the production of alkanes in Received in revised form non-native producing microorganisms using metabolic engineering strategies.
    [Show full text]
  • Lysobacter Enzymogenes
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Dissertations and Theses in Biological Sciences Biological Sciences, School of 8-2010 Detection Methods for the Genus Lysobacter and the Species Lysobacter enzymogenes Hu Yin University of Nebraska at Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/bioscidiss Part of the Life Sciences Commons Yin, Hu, "Detection Methods for the Genus Lysobacter and the Species Lysobacter enzymogenes" (2010). Dissertations and Theses in Biological Sciences. 15. https://digitalcommons.unl.edu/bioscidiss/15 This Article is brought to you for free and open access by the Biological Sciences, School of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Dissertations and Theses in Biological Sciences by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Detection Methods for the Genus Lysobacter and the Species Lysobacter enzymogenes By Hu Yin A THESIS Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Master of Science Major: Biological Sciences Under the Supervision of Professor Gary Y. Yuen Lincoln, Nebraska August, 2010 Detection Methods for the Genus Lysobacter and the Species Lysobacter enzymogenes Hu Yin, M.S. University of Nebraska, 2010 Advisor: Gary Y. Yuen Strains of Lysobacter enzymogenes, a bacterial species with biocontrol activity, have been detected via 16S rDNA sequences in soil in different parts of the world. In most instances, however, their occurrence could not be confirmed by isolation, presumably because the species occurred in low numbers relative to faster-growing species of Bacillus or Pseudomonas.
    [Show full text]
  • Data Driven Modelling of a Chemically Defined Growth Medium For
    bioRxiv preprint doi: https://doi.org/10.1101/548891; this version posted February 13, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Data Driven Modelling of a Chemically Defined Growth Medium for Cupriavidus necator H16 Christopher C. Azubuike, Martin G. Edwards, Angharad M. R. Gatehouse and Thomas P. Howard School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle-upon-Tyne, United Kingdom Cupriavidus necator is a Gram-negative soil bacterium of ma- as a chassis capable of exploiting renewable feedstock for jor biotechnological interest. It is a producer of the bioplas- the biosynthesis of valuable products (7). More widely, the tic 3-polyhydroxybutyrate, has been exploited in bioremedia- genus is known to encode genes facilitating metabolism of tion processes, and it’s lithoautotrophic capabilities suggest it environmental pollutants such as aromatics and heavy metals may function as a microbial cell factory upgrading renewable making it a potential microbial remediator (8, 9, 17–19). resources to fuels and chemicals. It remains necessary however to develop appropriate experimental resources to permit con- As with any bacterium, the development of C. necator as trolled bioengineering and system optimisation of this micro- an industrial chassis requires appropriate tools for studying bial chassis. A key resource for physiological, biochemical and and engineering the organism. One of these resources is metabolic studies of any microorganism is a chemically defined the availability of a characterised, chemically defined growth growth medium.
    [Show full text]
  • Draft Genome of a Heavy-Metal-Resistant Bacterium, Cupriavidus Sp
    Korean Journal of Microbiology (2020) Vol. 56, No. 3, pp. 343-346 pISSN 0440-2413 DOI https://doi.org/10.7845/kjm.2020.0061 eISSN 2383-9902 Copyright ⓒ 2020, The Microbiological Society of Korea Draft genome of a heavy-metal-resistant bacterium, Cupriavidus sp. strain SW-Y-13, isolated from river water in Korea Kiwoon Baek , Young Ho Nam , Eu Jin Chung , and Ahyoung Choi* Nakdonggang National Institute of Biological Resources (NNIBR), Sangju 37242, Republic of Korea 강물에서 분리한 중금속 내성 세균 Cupriavidus sp. SW-Y-13 균주의 유전체 해독 백기운 ･ 남영호 ･ 정유진 ･ 최아영* 국립낙동강생물자원관 담수생물연구본부 (Received July 6, 2020; Revised September 18, 2020; Accepted September 18, 2020) Cupriavidus sp. strain SW-Y-13 is an aerobic, Gram-negative, found to survive in close association with pollution-causing rod-shaped bacterium isolated from river water in South Korea, heavy metals, for example, Cupriavidus metallidurans, which in 2019. Its draft genome was produced using the PacBio RS II successfully grows in the presence of Cu, Hg, Ni, Ag, Cd, Co, platform and is thought to consist of five circular chromosomes Zn, and As (Goris et al., 2001; Vandamme and Coenye, 2004; with a total of 7,307,793 bp. The genome has a G + C content Janssen et al., 2010). Several bacteria found in polluted of 63.1%. Based on 16S rRNA sequence similarity, strain SW-Y-13 is most closely related to Cupriavidus metallidurans environments have been shown to adapt to the presence of toxic (98.4%). Genome annotation revealed that the genome is heavy metals. Identification of novel bacterial mechanisms comprised of 6,613 genes, 6,536 CDSs, 12 rRNAs, 61 tRNAs, facilitating growth in heavy-metal-polluted environments and 4 ncRNAs.
    [Show full text]
  • Cupriavidus Cauae Sp. Nov., Isolated from Blood of an Immunocompromised Patient
    TAXONOMIC DESCRIPTION Kweon et al., Int. J. Syst. Evol. Microbiol. 2021;71:004759 DOI 10.1099/ijsem.0.004759 Cupriavidus cauae sp. nov., isolated from blood of an immunocompromised patient Oh Joo Kweon1†, Wenting Ruan2†, Shehzad Abid Khan2, Yong Kwan Lim1, Hye Ryoun Kim1, Che Ok Jeon2,* and Mi- Kyung Lee1,* Abstract A novel Gram- stain- negative, facultative aerobic and rod- shaped bacterium, designated as MKL-01T and isolated from the blood of immunocompromised patient, was genotypically and phenotypically characterized. The colonies were found to be creamy yellow and convex. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences revealed that strain MKL-01T was most closely related to Cupriavidus gilardii LMG 5886T, present within a large cluster in the genus Cupriavidus. The genome sequence of strain MKL-01T showed the highest average nucleotide identity value of 92.1 % and digital DNA–DNA hybridization value of 44.8 % with the closely related species C. gilardii LMG 5886T. The genome size of the isolate was 5 750 268 bp, with a G+C content of 67.87 mol%. The strain could grow at 10–45 °C (optimum, 37–40 °C), in the presence of 0–10 % (w/v) NaCl (optimum, 0.5%) and at pH 6.0–10.0 (optimum, pH 7.0). Strain MKL-01T was positive for catalase and negative for oxidase. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c and/or C16 : 1 ω6c/C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c).
    [Show full text]
  • Phosphoglycolate Salvage in a Chemolithoautotroph Using the Calvin Cycle
    Phosphoglycolate salvage in a chemolithoautotroph using the Calvin cycle Nico J. Claassensa,1, Giovanni Scarincia,1, Axel Fischera, Avi I. Flamholzb, William Newella, Stefan Frielingsdorfc, Oliver Lenzc, and Arren Bar-Evena,2 aSystems and Synthetic Metabolism Lab, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; bDepartment of Molecular and Cell Biology, University of California, Berkeley, CA 94720; and cInstitut für Chemie, Physikalische Chemie, Technische Universität Berlin, 10623 Berlin, Germany Edited by Donald R. Ort, University of Illinois at Urbana–Champaign, Urbana, IL, and approved July 24, 2020 (received for review June 14, 2020) Carbon fixation via the Calvin cycle is constrained by the side In the cyanobacterium Synechocystis sp. PCC6803, gene dele- activity of Rubisco with dioxygen, generating 2-phosphoglycolate. tion studies were used to demonstrate the activity of two pho- The metabolic recycling of phosphoglycolate was extensively torespiratory routes in addition to the C2 cycle (5, 8). In the studied in photoautotrophic organisms, including plants, algae, glycerate pathway, two glyoxylate molecules are condensed to and cyanobacteria, where it is referred to as photorespiration. tartronate semialdehyde, which is subsequently reduced to glyc- While receiving little attention so far, aerobic chemolithoautotro- erate and phosphorylated to 3PG (Fig. 1). Alternatively, in the phic bacteria that operate the Calvin cycle independent of light oxalate decarboxylation pathway, glyoxylate is oxidized
    [Show full text]
  • Arenimonas Halophila Sp. Nov., Isolated from Soil
    TAXONOMIC DESCRIPTION Kanjanasuntree et al., Int J Syst Evol Microbiol 2018;68:2188–2193 DOI 10.1099/ijsem.0.002801 Arenimonas halophila sp. nov., isolated from soil Rungravee Kanjanasuntree,1 Jong-Hwa Kim,1 Jung-Hoon Yoon,2 Ampaitip Sukhoom,3 Duangporn Kantachote3 and Wonyong Kim1,* Abstract A Gram-staining-negative, aerobic, non-motile, rod-shaped bacterium, designated CAU 1453T, was isolated from soil and its taxonomic position was investigated using a polyphasic approach. Strain CAU 1453T grew optimally at 30 C and at pH 6.5 in the presence of 1 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that CAU 1453T represented a member of the genus Arenimonas and was most closely related to Arenimonas donghaensis KACC 11381T (97.2 % similarity). T CAU 1453 contained ubiquinone-8 (Q-8) as the predominant isoprenoid quinone and iso-C15 : 0 and iso-C16 : 0 as the major cellular fatty acids. The polar lipids consisted of diphosphatidylglycerol, a phosphoglycolipid, an aminophospholipid, two unidentified phospholipids and two unidentified glycolipids. CAU 1453T showed low DNA–DNA relatedness with the most closely related strain, A. donghaensis KACC 11381T (26.5 %). The DNA G+C content was 67.3 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, CAU 1453T represents a novel species of the genus Arenimonas, for which the name Arenimonas halophila sp. nov. is proposed. The type strain is CAU 1453T (=KCTC 62235T=NBRC 113093T). The genus Arenimonas, a member of the family Xantho- CAU 1453T was isolated from soil by the dilution plating monadaceae in the class Gammaproteobacteria was pro- method using marine agar 2216 (MA; Difco) [14].
    [Show full text]
  • Lysobacter, a New Genus of Nonhiting, Gliding Bacteria with a High Base Ratio
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1978, p. 367-393 Vol. 28, 3 0020-7713/78/0028-0367$02.00/0 No. Copyright 0 1978 International Association of Microbiological Societies Printed in U.S. A. Lysobacter, a New Genus of Nonhiting, Gliding Bacteria with a High Base Ratio PENELOPE CHRISTENSEN AND F. D. COOK Department of Microbiology, University of Alberta, Edmonton, Alberta, Canada Highly mucoid, cream, pink and yellow-brown gliding organisms having deoxy- ribonucleic acid guanine-plus-cytosine contents of 62 to 70.1 mol% have been isolated by several workers, but since these organisms have never been observed to produce typical myxobacterial fruiting bodies, their taxonomy has been prob- lematical. Forty-six isolates were studied in detail, among them Ensign and Wolfe’s organism AL-1 and Cook’s isolate 495, both of which produce important proteases, as well as Cook’s culture 3C, which elaborates the potent, wide- spectrum antibiotic myxin. A new genus, Lysobacter, has been established for these organisms, and four new species and one new subspecies have been named and described: L. antibioticus (type strain, ATCC 29479), L. brunescens (type strain, ATCC 29482), L. enzymogenes (type strain, ATCC 29487), L. enzymogenes subspecies cookii Christensen (type strain, ATCC 29488), and L. gummosus (type strain, ATCC 29489). The dimensions of the thin, gliding, flexing cells of Lyso- bacter are 0.3 to 0.5 by 1.0 to 15.0 (sometimes up to 70) pm. These soil and water organisms all degrade chitin, two degrade alginate, three degrade pectate, three degrade carboxymethylcellulose, and one degrades starch, but none decomposes filter paper or agar.
    [Show full text]
  • The Soil Microbial Food Web Revisited: Predatory Myxobacteria As Keystone Taxa?
    The ISME Journal https://doi.org/10.1038/s41396-021-00958-2 ARTICLE The soil microbial food web revisited: Predatory myxobacteria as keystone taxa? 1 1 1,2 1 1 Sebastian Petters ● Verena Groß ● Andrea Söllinger ● Michelle Pichler ● Anne Reinhard ● 1 1 Mia Maria Bengtsson ● Tim Urich Received: 4 October 2018 / Revised: 24 February 2021 / Accepted: 4 March 2021 © The Author(s) 2021. This article is published with open access Abstract Trophic interactions are crucial for carbon cycling in food webs. Traditionally, eukaryotic micropredators are considered the major micropredators of bacteria in soils, although bacteria like myxobacteria and Bdellovibrio are also known bacterivores. Until recently, it was impossible to assess the abundance of prokaryotes and eukaryotes in soil food webs simultaneously. Using metatranscriptomic three-domain community profiling we identified pro- and eukaryotic micropredators in 11 European mineral and organic soils from different climes. Myxobacteria comprised 1.5–9.7% of all obtained SSU rRNA transcripts and more than 60% of all identified potential bacterivores in most soils. The name-giving and well-characterized fi 1234567890();,: 1234567890();,: predatory bacteria af liated with the Myxococcaceae were barely present, while Haliangiaceae and Polyangiaceae dominated. In predation assays, representatives of the latter showed prey spectra as broad as the Myxococcaceae. 18S rRNA transcripts from eukaryotic micropredators, like amoeba and nematodes, were generally less abundant than myxobacterial 16S rRNA transcripts, especially in mineral soils. Although SSU rRNA does not directly reflect organismic abundance, our findings indicate that myxobacteria could be keystone taxa in the soil microbial food web, with potential impact on prokaryotic community composition.
    [Show full text]
  • Phylogenomics Insights Into Order and Families of Lysobacterales
    SHORT COMMUNICATION Kumar et al., Access Microbiology 2019;1 DOI 10.1099/acmi.0.000015 Phylogenomics insights into order and families of Lysobacterales Sanjeet Kumar†, Kanika Bansal, Prashant P. Patil‡ and Prabhu B. Patil* Abstract Order Lysobacterales (earlier known Xanthomonadales) is a taxonomically complex group of a large number of gamma-pro- teobacteria classified in two different families, namelyLysobacteraceae and Rhodanobacteraceae. Current taxonomy is largely based on classical approaches and is devoid of whole-genome information-based analysis. In the present study, we have taken all classified and poorly described species belonging to the order Lysobacterales to perform a phylogenetic analysis based on the 16 S rRNA sequence. Moreover, to obtain robust phylogeny, we have generated whole-genome sequencing data of six type species namely Metallibacterium scheffleri, Panacagrimonas perspica, Thermomonas haemolytica, Fulvimonas soli, Pseudoful- vimonas gallinarii and Rhodanobacter lindaniclasticus of the families Lysobacteraceae and Rhodanobacteraceae. Interestingly, whole-genome-based phylogenetic analysis revealed unusual positioning of the type species Pseudofulvimonas, Panacagri- monas, Metallibacterium and Aquimonas at family level. Whole-genome-based phylogeny involving 92 type strains resolved the taxonomic positioning by reshuffling the genus across families Lysobacteraceae and Rhodanobacteraceae. The present study reveals the need and scope for genome-based phylogenetic and comparative studies in order to address relationships of genera and species of order Lysobacterales. IMPact StatEMENT genus with unary species can serve as a reference and standard Species of order Lysobacterales have undergone several reclas- to compare later identified species of the respective genera. sifications, until today the taxonomy position of species within the order is largely devoid of whole-genome information.
    [Show full text]
  • Transcriptome Differences Between Cupriavidus Necator NH9 Grown with 3-Chlorobenzoate and That Grown with Benzoate
    Transcriptome differences between Cupriavidus necator NH9 grown with 3-chlorobenzoate and that grown with benzoate Ryota Moriuchi Shizuoka Daigaku Hideo Dohra Shizuoka Daigaku Yu Kanesaki Shizuoka Daigaku Naoto Ogawa ( [email protected] ) Shizuoka Daigaku Research article Keywords: 3-chlorobenzoate, Aromatic degradation, Benzoate, Chemotaxis, Cupriavidus, RNA-seq, Stress response, Transcriptome, Transporter Posted Date: November 10th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-50641/v3 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published at Bioscience, Biotechnology, and Biochemistry on March 15th, 2021. See the published version at https://doi.org/10.1093/bbb/zbab044. Page 1/22 Abstract Background Aromatic compounds derived from human activities are often released into the environment. Many of them, especially halogenated aromatics, are persistent in nature and pose threats to organisms. Therefore, the microbial degradation of these compounds has been studied intensively. Our laboratory has studied the expression of genes in Cupriavidus necator NH9 involved in the degradation of 3-chlorobenzoate (3-CB), a model compound for studies on bacterial degradation of chlorinated aromatic compounds. In this study aimed at exploring how this bacterium has adapted to the utilization of chlorinated aromatic compounds, we performed RNA-seq analysis of NH9 cells cultured with 3-CB, benzoate (BA), or citric acid (CA). The
    [Show full text]
  • A002 Methylobacterium Carri Sp. Nov., Isolated from Automotive Air
    A002 Methylobacterium carri sp. nov., Isolated from Automotive Air Conditioning System Jigwan Son and Jong-Ok Ka* Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University A bacterial strain, designated DB0501T, with Gram-stain-negative, aerobic, motile, and rod-shaped cell, was isolated from an automotive air conditioning system collected in the Republic of Korea. 16S rRNA gene sequence analysis indicated that the strain DB0501T grouped in the genus Methylobacterium and closely related to Methylobacterium platani PMB02T (98.8%), Methylobacterium currus PR1016AT (97.7%), Methylobacterium variabile DSM 16961T (97.7%), Methylobacterium aquaticum DSM 16371T (97.6%), Methylobacterium tarhaniae N4211T (97.4%) and Methylobacterium frigidaeris IER25-16T (97.2%). Genomic relatedness between strain DB0501T and its closest relatives was evaluated using average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity with values of 86.4–90.8%, 39.3 ± 2.6–48.2 ± 5.0% and 87.8–89.5% respectively. The strain grew 15-30°C , pH 5.5-8.0 and in 0–1.0% w/v NaCl. Summed feature 3 (C16:1 7c and/or C16:1 6c) and summed feature 8 (C18:1 ω7c T and/or C18:1 ω6c) were the predominant cellular fatty acids in strain DB0501 . Q-10 was the major ubiquinone. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylcholine. The DNA G+C content of strain DB0501T was 70.8 mol%. Based on phenotypic, genotypic and chemotaxonomic data, strain DB0501T represents a novel species of the genus Methylobacterium, for which the name Methylobacterium carri sp.
    [Show full text]