DOCSLIB.ORG

EMBRIC (Grant Agreement No

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
EMBRIC (Grant Agreement No Deliverable D6.1 EMBRIC (Grant Agreement No. 654008) Grant Agreement Number: 654008 EMBRIC European Marine Biological Research Infrastructure Cluster to promote the Blue Bioeconomy Horizon 2020 – the Framework Programme for Research and Innovation (2014-2020), H2020-INFRADEV-1-2014-1 Start Date of Project: 01.06.2015 Duration: 48 Months Deliverable D6.1 EMBRIC showcases: prototype pipelines from the microorganism to product discovery (M36) HORIZON 2020 - INFRADEV Deliverable D6.1 EMBRIC showcases: prototype pipelines from the microorganism to product discovery Page 1 of 85 Deliverable D6.1 EMBRIC (Grant Agreement No. 654008) Implementation and operation of cross-cutting services and solutions for clusters of ESFRI Grant agreement no.: 654008 Project acronym: EMBRIC Project website: www.embric.eu Project full title: European Marine Biological Research Infrastructure cluster to promote the Bioeconomy Project start date: June 2015 (48 months) Submission due date : May 2018 Actual submission date: May 2018 Work Package: WP 6 Microbial pipeline from environment to active compounds Lead Beneficiary: CABI Version: 9.0 Authors: SMITH David GOSS Rebecca OVERMANN Jörg BRÖNSTRUP Mark PASCUAL Javier BAJERSKI Felizitas HENSLER Michael WANG Yunpeng ABRAHAM Emily Deliverable D6.1 EMBRIC showcases: prototype pipelines from the microorganism to product discovery Page 2 of 85 Deliverable D6.1 EMBRIC (Grant Agreement No. 654008) Project funded by the European Union’s Horizon 2020 research and innovation programme (2015-2019) Dissemination Level PU Public PP Restricted to other programme participants (including the Commission Services) RE Restricted to a group specified by the consortium (including the Commission Services) CO Confidential, only for members of the consortium (including the Commission X Services Deliverable D6.1 EMBRIC showcases: prototype pipelines from the microorganism to product discovery Page 3 of 85 Deliverable D6.1 EMBRIC (Grant Agreement No. 654008) Abstract The objective is to develop coherent chains of high quality services for access to biological, analytical and data resources and deploying common underpinning technologies and practices for the route to useful compounds from marine bacteria. This prototype pipeline brings together the expertise and facilities of partners from the MIRRI, EMBRC and EUOPENSCREEN research infrastructures to target and release the potential of microorganisms from isolation, through characterisation, to end product. Bacteria are key components of the marine environment, performing a wide range of biogeochemical and ecological functions yet we know very little about them. It is estimated that we have seen less than 1 percent in culture and the vast potential remains locked away. Molecular ecology has provided us with a picture of what might be there and an idea of the chemistry they may perform. The pipeline aimed to unlock this potential, utilizing the specialist expertise and facilities of consortium laboratories, organisms difficult to cultivate or have yet to be grown were targeted, characterised and prepared for scale up and production of active compounds. DSMZ undertook the task to make difficult-to-culture bacterial strains amenable to subsequent natural compound analyses. Optimal growth conditions for some of these organisms were determined and as a result bacterial strains with novel properties were isolated and grown. Following de-replicating of potential clones DSMZ isolated 264 species of slow growing bacteria from seawater, sediment and sponges of the Pacific Ocean representing the phyla Actinobacteria, Bacteroidetes, Proteobacteria and Rhodothermaeota. The most interesting of these will be selected for cosmid library production two Arcobacter species were fermented and organic extracts supplied to HZI for analysis. USTAN had the role of improving the efficiency and effectiveness of a harmonised natural product discovery pipeline. Cosmid libraries were established for test strains and these put through heterologous platforms to determine the presence of compounds. Nine gene clusters and a series of compounds were detected. Improvements to the process were made using elicitors and promoters and some difficult cyclic peptides were characterised. HZI improved the efficiency of different extraction and characterization techniques for use on different types of organisms and as a result isolates producing interesting compounds were discovered. Once the pipeline through the partner infrastructures was fine-tuned, fully sequenced samples were put through the pipeline and it was demonstrated that interesting compounds could be discovered. CABI focused on the regulatory environment addressing issues around access to genetic resources. The prototype pipeline resulted in a flexible system to access cross research Infrastructure expertise and facilities to meet specific user defined demand of the research community. In one single experiment to develop the EMBRIC microbial prototype pipeline, 264 rarely isolated species of bacteria were made available for study of their bioactive compounds. This demonstrates that coordinated and targeted isolation programmes engaging research teams from the many partners in the Research Infrastructures orchestrated for specific bioindustry needs could yield many thousands of candidate organisms. The potential for discovery of new interesting bioactive compounds is thus increased exponentially. Deliverable D6.1 EMBRIC showcases: prototype pipelines from the microorganism to product discovery Page 4 of 85 Deliverable D6.1 EMBRIC (Grant Agreement No. 654008) Contents Abstract 4 1. Introduction 7 1.1 Microorganism prototype pipeline 7 2. Protocols for isolation, selection, growth of strains and extract supply 11 2.1. Sample collection and processing 11 2.3. Taxonomic affiliation of isolates 14 2.4. Maintenance procedures 14 2.5. Fermentation of bacteria for natural product production 15 3. The genomic characterisation, cosmid library production and analysis 16 3.1 Gene Clusters Prediction 16 3.2 Genomic DNA Preparation 16 3.3 Vector DNA Preparation 17 3.4 Construction of Cosmid Library 18 3.5 Transformation of Gene Clusters and Secondary Metabolite Heterologous Expression 19 4. Analysis of extracts 22 4.1 Analysis of extracts at USTAN 22 4.2 Analysis of extracts at HZI 23 5. Regulatory Environment 26 5.1 Regulatory Guidance and Community Best Practices 28 5.2 Regulations impacting on collection, handling, use and distribution of organisms 31 5.3 Health and Safety 32 5.4 Microorganisms as hazardous substances 33 5.5 Classification of Microorganisms on the Basis of Hazard 33 5.6 Quarantine regulations 35 5.7 Postal Regulations and Safety 35 5.8 Packaging 36 5.9 Regulations governing distribution of cultures 36 5.10 Control of Distribution of Dangerous Organisms 36 5.11 Biological Weapons Convention 37 5.12 Export Licensing Measures 37 5.13 Control procedures: UKNCC control of Dangerous Pathogens 39 5.14 Convention on Biological Diversity 40 5.15 Ownership of Intellectual Property Rights (IPR) 40 Deliverable D6.1 EMBRIC showcases: prototype pipelines from the microorganism to product discovery Page 5 of 85 Deliverable D6.1 EMBRIC (Grant Agreement No. 654008) 5.16 Safety information provided to the recipient of microorganisms 41 5.17 Areas Beyond National Jurisdiction (ABNJ) 42 6. Outputs from the microorganism prototype pipeline 45 6.1 Strains collected from the Pacific Ocean by DSMZ 45 6.2 Cosmid libraries and biosynthetic gene clusters at USTAN 45 6.3 Characterisation of extracts at HZI 61 6.4 Significance of outputs 64 7. EMBRIC pathways to discovery 66 8. Summary 75 9. References and bibliography 77 Deliverable D6.1 EMBRIC showcases: prototype pipelines from the microorganism to product discovery Page 6 of 85 Deliverable D6.1 EMBRIC (Grant Agreement No. 654008) 1. Introduction The European Marine Biological Research Infrastructure Cluster (EMBRIC) is designed to accelerate the pace of scientific discovery and innovation from marine Bio-Resources. EMBRIC aims to promote new applications derived from marine organisms in fields such as drug discovery, novel foods and food ingredients, aquaculture selective breeding, bioremediation, cosmetics and bioenergy (http://www.embric.eu/). Researchers design their own experiments to lead to discovery of novel properties or products but such programmes can be enhanced by using the facilities available through European Research Infrastructures. EMBRIC addresses the steps to discovery from selection and isolation of the marine microorganisms to the characterisation and isolation of bioactive compounds. EMBRIC tests the different routes that can be followed and demonstrates the advantages of engaging with the most appropriate technologies available. Additionally, there are numerous areas where policy, regulations or legislation impact on the isolation, use and distribution of organisms which include health and safety, quarantine regulations, shipping, packaging, governing distribution of cultures including dangerous pathogens, export licensing measures, ownership of Intellectual Property Rights (IPR) and more. Compliance with this regulatory environment may be complicated and ever changing but it is not new. Individuals and their Institutions must address this but in many cases community best practices or common approaches have helped them. For example culture collections through the European Culture Collections’ Organisation (ECCO) and the World Federation for Culture Collections (WFCC) have supported their members in compliance
Load more

Recommended publications
  • Motiliproteus Sediminis Gen. Nov., Sp. Nov., Isolated from Coastal Sediment
    Antonie van Leeuwenhoek (2014) 106:615–621 DOI 10.1007/s10482-014-0232-2 ORIGINAL PAPER Motiliproteus sediminis gen. nov., sp. nov., isolated from coastal sediment Zong-Jie Wang • Zhi-Hong Xie • Chao Wang • Zong-Jun Du • Guan-Jun Chen Received: 3 April 2014 / Accepted: 4 July 2014 / Published online: 20 July 2014 Ó Springer International Publishing Switzerland 2014 Abstract A novel Gram-stain-negative, rod-to- demonstrated that the novel isolate was 93.3 % similar spiral-shaped, oxidase- and catalase- positive and to the type strain of Neptunomonas antarctica, 93.2 % facultatively aerobic bacterium, designated HS6T, was to Neptunomonas japonicum and 93.1 % to Marino- isolated from marine sediment of Yellow Sea, China. bacterium rhizophilum, the closest cultivated rela- It can reduce nitrate to nitrite and grow well in marine tives. The polar lipid profile of the novel strain broth 2216 (MB, Hope Biol-Technology Co., Ltd) consisted of phosphatidylethanolamine, phosphatidyl- with an optimal temperature for growth of 30–33 °C glycerol and some other unknown lipids. Major (range 12–45 °C) and in the presence of 2–3 % (w/v) cellular fatty acids were summed feature 3 (C16:1 NaCl (range 0.5–7 %, w/v). The pH range for growth x7c/iso-C15:0 2-OH), C18:1 x7c and C16:0 and the main was pH 6.2–9.0, with an optimum at 6.5–7.0. Phylo- respiratory quinone was Q-8. The DNA G?C content genetic analysis based on 16S rRNA gene sequences of strain HS6T was 61.2 mol %. Based on the phylogenetic, physiological and biochemical charac- teristics, strain HS6T represents a novel genus and The GenBank accession number for the 16S rRNA gene T species and the name Motiliproteus sediminis gen.
    [Show full text]
  • Genetic Diversity of Culturable Vibrio in an Australian Blue Mussel Mytilus Galloprovincialis Hatchery
    Vol. 116: 37–46, 2015 DISEASES OF AQUATIC ORGANISMS Published September 17 doi: 10.3354/dao02905 Dis Aquat Org Genetic diversity of culturable Vibrio in an Australian blue mussel Mytilus galloprovincialis hatchery Tzu Nin Kwan*, Christopher J. S. Bolch National Centre for Marine Conservation and Resource Sustainability, University of Tasmania, Locked Bag 1370, Newnham, Tasmania 7250, Australia ABSTRACT: Bacillary necrosis associated with Vibrio species is the common cause of larval and spat mortality during commercial production of Australian blue mussel Mytilus galloprovincialis. A total of 87 randomly selected Vibrio isolates from various stages of rearing in a commercial mus- sel hatchery were characterised using partial sequences of the ATP synthase alpha subunit gene (atpA). The sequenced isolates represented 40 unique atpA genotypes, overwhelmingly domi- nated (98%) by V. splendidus group genotypes, with 1 V. harveyi group genotype also detected. The V. splendidus group sequences formed 5 moderately supported clusters allied with V. splen- didus/V. lentus, V. atlanticus, V. tasmaniensis, V. cyclitrophicus and V. toranzoniae. All water sources showed considerable atpA gene diversity among Vibrio isolates, with 30 to 60% of unique isolates recovered from each source. Over half (53%) of Vibrio atpA genotypes were detected only once, and only 7 genotypes were recovered from multiple sources. Comparisons of phylogenetic diversity using UniFrac analysis showed that the culturable Vibrio community from intake, header, broodstock and larval tanks were phylogenetically similar, while spat tank communities were different. Culturable Vibrio associated with spat tank seawater differed in being dominated by V. toranzoniae-affiliated genotypes. The high diversity of V. splendidus group genotypes detected in this study reinforces the dynamic nature of microbial communities associated with hatchery culture and complicates our efforts to elucidate the role of V.
    [Show full text]
  • First Evidence for a Vibrio Strain Pathogenic to Mytilus Edulis Altering Hemocyte Immune Capacities
    1 Developmental & Comparative Immunology Achimer April 2016, Volume 57, Pages 107-119 http://dx.doi.org/10.1016/j.dci.2015.12.014 http://archimer.ifremer.fr http://archimer.ifremer.fr/doc/00302/41336/ © 2015 Elsevier Ltd. All rights reserved First evidence for a Vibrio strain pathogenic to Mytilus edulis altering hemocyte immune capacities Ben Cheikh Yosra 1, Travers Marie-Agnes 2, Morga Benjamin 2, Godfrin Yoann 2, Rioult Damien 3, Le Foll Frank 1, * 1 Laboratory of Ecotoxicology- Aquatic Environments, UMR-I 02, SEBIO, University of Le Havre, F- 76063, Le Havre Cedex, France 2 Ifremer, SG2M-LGPMM, Laboratoire de Génétique et Pathologie des Mollusques Marins, Avenue de Mus de Loup, 17390, La Tremblade, France 3 Laboratory of Ecotoxicology- Aquatic Environments, UMR-I 02, SEBIO, University of Reims Champagne Ardenne, Campus Moulin de la House, F-51100, Reims, France * Corresponding author : Frank Le Foll, email address : [email protected] Abstract : Bacterial isolates were obtained from mortality events affecting Mytilus edulis and reported by professionals in 2010–2013 or from mussel microflora. Experimental infections allowed the selection of two isolates affiliated to Vibrio splendidus/Vibrio hemicentroti type strains: a virulent 10/068 1T1 (76.6% and 90% mortalities in 24 h and 96 h) and an innocuous 12/056 M24T1 (0% and 23.3% in 24 h and 96 h). These two strains were GFP-tagged and validated for their growth characteristics and virulence as genuine models for exposure. Then, host cellular immune responses to the microbial invaders were assessed. In the presence of the virulent strain, hemocyte motility was instantaneously enhanced but markedly slowed down after 2 h exposure.
    [Show full text]
  • Aquatic Microbial Ecology 80:15
    The following supplement accompanies the article Isolates as models to study bacterial ecophysiology and biogeochemistry Åke Hagström*, Farooq Azam, Carlo Berg, Ulla Li Zweifel *Corresponding author: [email protected] Aquatic Microbial Ecology 80: 15–27 (2017) Supplementary Materials & Methods The bacteria characterized in this study were collected from sites at three different sea areas; the Northern Baltic Sea (63°30’N, 19°48’E), Northwest Mediterranean Sea (43°41'N, 7°19'E) and Southern California Bight (32°53'N, 117°15'W). Seawater was spread onto Zobell agar plates or marine agar plates (DIFCO) and incubated at in situ temperature. Colonies were picked and plate- purified before being frozen in liquid medium with 20% glycerol. The collection represents aerobic heterotrophic bacteria from pelagic waters. Bacteria were grown in media according to their physiological needs of salinity. Isolates from the Baltic Sea were grown on Zobell media (ZoBELL, 1941) (800 ml filtered seawater from the Baltic, 200 ml Milli-Q water, 5g Bacto-peptone, 1g Bacto-yeast extract). Isolates from the Mediterranean Sea and the Southern California Bight were grown on marine agar or marine broth (DIFCO laboratories). The optimal temperature for growth was determined by growing each isolate in 4ml of appropriate media at 5, 10, 15, 20, 25, 30, 35, 40, 45 and 50o C with gentle shaking. Growth was measured by an increase in absorbance at 550nm. Statistical analyses The influence of temperature, geographical origin and taxonomic affiliation on growth rates was assessed by a two-way analysis of variance (ANOVA) in R (http://www.r-project.org/) and the “car” package.
    [Show full text]
  • D 6.1 EMBRIC Showcases
    Grant Agreement Number: 654008 EMBRIC European Marine Biological Research Infrastructure Cluster to promote the Blue Bioeconomy Horizon 2020 – the Framework Programme for Research and Innovation (2014-2020), H2020-INFRADEV-1-2014-1 Start Date of Project: 01.06.2015 Duration: 48 Months Deliverable D6.1 b EMBRIC showcases: prototype pipelines from the microorganism to product discovery (Revised 2019) HORIZON 2020 - INFRADEV Implementation and operation of cross-cutting services and solutions for clusters of ESFRI 1 Grant agreement no.: 654008 Project acronym: EMBRIC Project website: www.embric.eu Project full title: European Marine Biological Research Infrastructure cluster to promote the Bioeconomy (Revised 2019) Project start date: June 2015 (48 months) Submission due date: May 2019 Actual submission date: Apr 2019 Work Package: WP 6 Microbial pipeline from environment to active compounds Lead Beneficiary: CABI [Partner 15] Version: 1.0 Authors: SMITH David [CABI Partner 15] GOSS Rebecca [USTAN 10] OVERMANN Jörg [DSMZ Partner 24] BRÖNSTRUP Mark [HZI Partner 18] PASCUAL Javier [DSMZ Partner 24] BAJERSKI Felizitas [DSMZ Partner 24] HENSLER Michael [HZI Partner 18] WANG Yunpeng [USTAN Partner 10] ABRAHAM Emily [USTAN Partner 10] FIORINI Federica [HZI Partner 18] Project funded by the European Union’s Horizon 2020 research and innovation programme (2015-2019) Dissemination Level PU Public X PP Restricted to other programme participants (including the Commission Services) RE Restricted to a group specified by the consortium (including the Commission Services) CO Confidential, only for members of the consortium (including the Commission Services 2 Abstract Deliverable D6.1b replaces Deliverable 6.1 EMBRIC showcases: prototype pipelines from the microorganism to product discovery with the specific goal to refine technologies used but more specifically deliver results of the microbial discovery pipeline.
    [Show full text]
  • Microbial Degradation of Organic Micropollutants in Hyporheic Zone Sediments
    Microbial degradation of organic micropollutants in hyporheic zone sediments Dissertation To obtain the Academic Degree Doctor rerum naturalium (Dr. rer. nat.) Submitted to the Faculty of Biology, Chemistry, and Geosciences of the University of Bayreuth by Cyrus Rutere Bayreuth, May 2020 This doctoral thesis was prepared at the Department of Ecological Microbiology – University of Bayreuth and AG Horn – Institute of Microbiology, Leibniz University Hannover, from August 2015 until April 2020, and was supervised by Prof. Dr. Marcus. A. Horn. This is a full reprint of the dissertation submitted to obtain the academic degree of Doctor of Natural Sciences (Dr. rer. nat.) and approved by the Faculty of Biology, Chemistry, and Geosciences of the University of Bayreuth. Date of submission: 11. May 2020 Date of defense: 23. July 2020 Acting dean: Prof. Dr. Matthias Breuning Doctoral committee: Prof. Dr. Marcus. A. Horn (reviewer) Prof. Harold L. Drake, PhD (reviewer) Prof. Dr. Gerhard Rambold (chairman) Prof. Dr. Stefan Peiffer In the battle between the stream and the rock, the stream always wins, not through strength but by perseverance. Harriett Jackson Brown Jr. CONTENTS CONTENTS CONTENTS ............................................................................................................................ i FIGURES.............................................................................................................................. vi TABLES ..............................................................................................................................
    [Show full text]
  • Vibrio Parahaemolyticus Host Pathogen
    FUNCTIONAL ANALYSIS OF THE ROLE OF ALTERNATIVE SIGMA FACTORS IN VIBRIO PARAHAEMOLYTICUS HOST PATHOGEN INTERACTIONS by Brandy L. Haines-Menges A dissertation submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Sciences Summer 2015 © 2015 Brandy Haines-Menges All Rights Reserved ProQuest Number: 3730237 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. ProQuest 3730237 Published by ProQuest LLC (2015). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code Microform Edition © ProQuest LLC. ProQuest LLC. 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, MI 48106 - 1346 FUNCTIONAL ANALYSIS OF THE ROLE OF ALTERNATIVE SIGMA FACTORS IN VIBRIO PARAHAEMOLYTICUS HOST PATHOGEN INTERACTIONS by Brandy L. Haines-Menges Approved: __________________________________________________________ Robin W. Morgan, Ph.D. Chair of the Department of Biological Sciences Approved: __________________________________________________________ George H. Watson, Ph.D. Dean of the College of Arts and Sciences Approved: __________________________________________________________ James G. Richards, Ph.D. Vice Provost for Graduate and Professional Education I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy.
    [Show full text]
  • Marinobacterium Coralli Sp. Nov., Isolated from Mucus of Coral (Mussismilia Hispida)
    International Journal of Systematic and Evolutionary Microbiology (2011), 61, 60–64 DOI 10.1099/ijs.0.021105-0 Marinobacterium coralli sp. nov., isolated from mucus of coral (Mussismilia hispida) Luciane A. Chimetto,1,2,3 Ilse Cleenwerck,3 Marcelo Brocchi,1 Anne Willems,4 Paul De Vos3,4 and Fabiano L. Thompson2 Correspondence 1Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Fabiano L. Thompson Campinas (UNICAMP), Brazil [email protected] 2Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Brazil 3BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium 4Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium A Gram-negative, aerobic bacterium, designated R-40509T, was isolated from mucus of the reef builder coral (Mussismilia hispida) located in the Sa˜o Sebastia˜o Channel, Sa˜o Paulo, Brazil. The + strain was oxidase-positive and catalase-negative, and required Na for growth. Its phylogenetic position was in the genus Marinobacterium and the closest related species were Marinobacterium sediminicola, Marinobacterium maritimum and Marinobacterium stanieri; the isolate exhibited 16S rRNA gene sequence similarities of 97.5–98.0 % with the type strains of these species. 16S rRNA gene sequence similarities with other type strains of the genus Marinobacterium were below 96 %. DNA–DNA hybridizations between strain R-40509T and the type strains of the phylogenetically closest species of the genus Marinobacterium revealed less than 70 % DNA–DNA relatedness, supporting the novel species status of the strain. Phenotypic characterization revealed that the strain was able to grow at 15–42 6C and in medium containing up to 9 % NaCl.
    [Show full text]
  • Ecological Roles of Arc Signal Transduction System Revealed by Evolutionary Genetics Analysis
    Open Access Journal of Bacteriology and Mycology Research Article Ecological Roles of Arc Signal Transduction System Revealed by Evolutionary Genetics Analysis Yangyang Dong, Fen Wan, Jianhua Yin and Haichun Gao* Abstract Institute of Microbiology and College of Life Sciences, The Arc signal transduction system was studied in γ-proteobacteria to Zhejiang University, China determine evolutionary mechanisms and ecological pressures responsible for *Corresponding author: Haichun Gao, Institute the plasticity of this system. Phylogenic analysis of the arcA gene encoding the of Microbiology and College of Life Sciences, Zhejiang DNA-binding response regulator suggests that the gene has remained under University, China strong purifying selection throughout its history while the arcB gene encoding the sensor histidine kinase has undergone extensive modification in various Received: August 14, 2014; Accepted: November 06, lineages. The major observed modification occurs in the Alteromonadaceae 2014; Published: November 12, 2014 family, where the Hpt domain of ArcB has been uncoupled from the sensor component in several genera (Shewanella, Colwellia and Idiomarina). This phenomenon appears to be linked to the free-living lifestyles of the Alteromonads. In contrast to the prevailing view of the Arc system existing only in facultative anaerobes, several of the Alteromonad species which encode Arc systems are strict aerobes or aero-tolerant anaerobes, suggesting additional functions for the Arc system beyond facultative anaerobiosis. Molecular clock estimates using linearized phylogenetics trees for the arcA gene place the origins of the system at 600-1300 million years ago, a period roughly corresponding to the rise in atmospheric oxygen levels that occurred in the Precambrian Era. It is hypothesized that the Arc system originated as an early oxidative stress response mechanism in the γ-proteobacteria and was later co-opted for the facultative anaerobic lifestyle.
    [Show full text]
  • Ramlibacter Alkalitolerans Sp. Nov., Alkali-Tolerant Bacterium Isolated from Soil of Ginseng
    TAXONOMIC DESCRIPTION Lee and Cha, Int J Syst Evol Microbiol 2017;67:4619–4623 DOI 10.1099/ijsem.0.002342 Ramlibacter alkalitolerans sp. nov., alkali-tolerant bacterium isolated from soil of ginseng Do-Hoon Lee and Chang-Jun Cha* Abstract A novel bacterial strain, designated CJ661T, was isolated from soil of ginseng in Anseong, South Korea. Cells of strain CJ661T were white-coloured, Gram-staining-negative, non-motile, aerobic and rod-shaped. Strain CJ661T grew optimally at 30 C and pH 7.0. The analysis of 16S rRNA gene sequence of strain CJ661T showed that it belongs to the genus Ramlibacter within the family Comamonadaceae and was most closely related to Ramlibacter ginsenosidimutans KCTC 22276T (98.1 %), followed by Ramlibacter henchirensis DSM 14656T (97.1 %). DNA–DNA relatedness levels of strain CJ661T were 40.6 % to R. ginsenosidimutans KCTC 22276T and 25.0 % to R. henchirensis DSM 14656T. The major isoprenoid quinone was ubiquinone (Q-8). The predominant polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The T major cellular fatty acids of strain CJ661 were summed feature 3 (C16 : 1 !6c and/or C16 : 1 !7c), C16 : 0 and summed feature 8 (C18 : 1 !7c and/or C18 : 1 !6c). The G+C content of the genomic DNA was 65.4 mol%. On the basis polyphasic taxonomic data, strain CJ661T represents a novel species in the genus Ramlibacter, for which name Ramlibacter alkalitolerans sp. nov. is proposed; the type strain is CJ661T (=KACC 19305T=JCM 32081T). The genus Ramlibacter was introduced by Heulin et al. [1], (Qiagen). The 16S rRNA gene sequence was determined at and belongs to the family Comamonadaceae in the class Solgent (Daejeon, Korea) using the BigDye Terminator Cycle Betaproteobacteria.
    [Show full text]
  • Mutation Is the Main Driving Force in the Diversification of the Vibrio Splendidus Clade
    Microbes Environ. Vol. 24, No. 4, 281–285, 2009 http://wwwsoc.nii.ac.jp/jsme2/ doi:10.1264/jsme2.ME09128 Mutation is the Main Driving Force in the Diversification of the Vibrio splendidus Clade TOMOO SAWABE1*, SHINICHI KOIZUMI1, YOUHEI FUKUI1, SATOSHI NAKAGAWA1, ELENA P. IVANOVA2,3, KUMIKO KITA-TSUKAMOTO4, KAZUHIRO KOGURE4, and FABIANO L. THOMPSON5 1Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3–1–1 Minato-cho, Hakodate 041–8611, Japan; 2Swinburne University of Technology, PO Box 218, Hawthorn, Victoria 3122, Australia; 3Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Vladivostok 690022, Pr. 100 Let Vladivostoku 159, Russian Federation; 4Ocean Research Institute, University of Tokyo, 1–15 Minamindai, Nakano-ku, Tokyo 164–8639, Japan; and 5Department of Genetics, Center of Health Sciences, Federal University of Rio de Janeiro, Ilha do Fundão, Caixa Postal 68011, CEP 21944–970, RJ, Brazil (Received May 18, 2009—Accepted July 30, 2009—Published online September 3, 2009) The Vibrio splendidus clade is the biggest in Vibrionales composed of 11 described species (25). Diversification of these species may have occurred 260 million years ago. The main driving forces of speciation in this clade have never been studied. Population biological parameters (population base recombination rate (ρ), population base mutation rate (θ), and index of association (Ia)) were determined among 16 strains of 9 defined species in the Splendidus cluster. A comparison of individual gene phylogeny indicated significant incongruence in tree topology, which suggests the occurrence of recombination between species. Homologous recombination between species was detected at four loci. However, the mutation rate θ was higher than the recombination rate ρ, suggesting that mutation is the main driving force in the diversification of V.
    [Show full text]
  • Repurposing a Chemosensory Macromolecular Machine
    Supplementary Information Repurposing a chemosensory macromolecular machine Ortega D. R. et. al. 1 Supplementary Discussion Our results also shed light on the biological function of CheD. CheD is thought to interact with chemoreceptors in an adaptation mechanism together with CheC and CheY1, but more recent results showed that CheD from Bacillus subtilis is able to deamidate chemoreceptors in vitro without CheC2. Our results provide two further pieces of evidence supporting the idea that CheD is able to perform a biological role independently of CheC. First, the ancestral F7 system included cheD but not cheC. Second, cheD co-evolved with the ancestral F7 cheY (it was lost in the same evolutionary step), pointing to a functional link. A recent study in Comamonas testosteroni, an organism with a stage 4 F7 system, shows that the kinase CheA is able to phosphorylate both the ancient CheY as well as the recently acquired CheY- F6-like3. Deletion of the CheY-F6-like protein completely abolished chemotaxis response, while the deletion of CheY-F7 only partially affected it. The study further shows that CheY-F7 has a much faster auto-dephosphorylation rate than CheY-F6-like. The authors interpreted these results such that the CheY-F6-like is the primary response regulator, and CheY-F7 may act as a phosphate sink. These conclusions are based on previous work in organisms with multiple CheY genes per chemosensory cluster. However, because CheY-F7 in stages 1 and 2 is the sole response regulator of the system, we hypothesize that it plays a major role in the control of a yet-unknown cellular process, at least in stages 1 and 2.
    [Show full text]