Characterisation of Diverse Microbial Communities and Application of Novel Detection Techniques
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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. -
Card Uses a Minor Groove Wedge Mechanism to Stabilize the RNA
1 CarD uses a minor groove wedge mechanism to stabilize the RNA 2 polymerase open promoter complex 3 4 Brian Bae1, James Chen1, Elizabeth Davis1, Katherine Leon1, Seth A. Darst1,*, 5 Elizabeth A. Campbell1,* 6 7 1The Rockefeller University, Laboratory for Molecular Biophysics, 1230 York Avenue, New York, 8 NY 10065, USA. 9 10 *Correspondence to: E-mail: [email protected], [email protected] 11 12 Present Address: Elizabeth Davis, The University of Minnesota School of Medicine, 13 420 Delaware St. SE, Minneapolis, MN 55455, USA; Katherine Leon, Department of 14 Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, GCIS 15 W219 Chicago, IL 60637, USA. 16 17 2 18 Abstract A key point to regulate gene expression is at transcription initiation, and 19 activators play a major role. CarD, an essential activator in Mycobacterium tuberculosis, 20 is found in many bacteria, including Thermus species, but absent in Escherichia coli. To 21 delineate the molecular mechanism of CarD, we determined crystal structures of 22 Thermus transcription initiation complexes containing CarD. The structures show CarD 23 interacts with the unique DNA topology presented by the upstream double- 24 stranded/single-stranded DNA junction of the transcription bubble. We confirm that our 25 structures correspond to functional activation complexes, and extend our understanding 26 of the role of a conserved CarD Trp residue that serves as a minor groove wedge, 27 preventing collapse of the transcription bubble to stabilize the transcription initiation 28 complex. Unlike E. coli RNAP, many bacterial RNAPs form unstable promoter 29 complexes, explaining the need for CarD. -
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. -
Systema Naturae. the Classification of Living Organisms
Systema Naturae. The classification of living organisms. c Alexey B. Shipunov v. 5.601 (June 26, 2007) Preface Most of researches agree that kingdom-level classification of living things needs the special rules and principles. Two approaches are possible: (a) tree- based, Hennigian approach will look for main dichotomies inside so-called “Tree of Life”; and (b) space-based, Linnaean approach will look for the key differences inside “Natural System” multidimensional “cloud”. Despite of clear advantages of tree-like approach (easy to develop rules and algorithms; trees are self-explaining), in many cases the space-based approach is still prefer- able, because it let us to summarize any kinds of taxonomically related da- ta and to compare different classifications quite easily. This approach also lead us to four-kingdom classification, but with different groups: Monera, Protista, Vegetabilia and Animalia, which represent different steps of in- creased complexity of living things, from simple prokaryotic cell to compound Nature Precedings : doi:10.1038/npre.2007.241.2 Posted 16 Aug 2007 eukaryotic cell and further to tissue/organ cell systems. The classification Only recent taxa. Viruses are not included. Abbreviations: incertae sedis (i.s.); pro parte (p.p.); sensu lato (s.l.); sedis mutabilis (sed.m.); sedis possi- bilis (sed.poss.); sensu stricto (s.str.); status mutabilis (stat.m.); quotes for “environmental” groups; asterisk for paraphyletic* taxa. 1 Regnum Monera Superphylum Archebacteria Phylum 1. Archebacteria Classis 1(1). Euryarcheota 1 2(2). Nanoarchaeota 3(3). Crenarchaeota 2 Superphylum Bacteria 3 Phylum 2. Firmicutes 4 Classis 1(4). Thermotogae sed.m. 2(5). -
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. -
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. -
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. -
Contents Topic 1. Introduction to Microbiology. the Subject and Tasks
Contents Topic 1. Introduction to microbiology. The subject and tasks of microbiology. A short historical essay………………………………………………………………5 Topic 2. Systematics and nomenclature of microorganisms……………………. 10 Topic 3. General characteristics of prokaryotic cells. Gram’s method ………...45 Topic 4. Principles of health protection and safety rules in the microbiological laboratory. Design, equipment, and working regimen of a microbiological laboratory………………………………………………………………………….162 Topic 5. Physiology of bacteria, fungi, viruses, mycoplasmas, rickettsia……...185 TOPIC 1. INTRODUCTION TO MICROBIOLOGY. THE SUBJECT AND TASKS OF MICROBIOLOGY. A SHORT HISTORICAL ESSAY. Contents 1. Subject, tasks and achievements of modern microbiology. 2. The role of microorganisms in human life. 3. Differentiation of microbiology in the industry. 4. Communication of microbiology with other sciences. 5. Periods in the development of microbiology. 6. The contribution of domestic scientists in the development of microbiology. 7. The value of microbiology in the system of training veterinarians. 8. Methods of studying microorganisms. Microbiology is a science, which study most shallow living creatures - microorganisms. Before inventing of microscope humanity was in dark about their existence. But during the centuries people could make use of processes vital activity of microbes for its needs. They could prepare a koumiss, alcohol, wine, vinegar, bread, and other products. During many centuries the nature of fermentations remained incomprehensible. Microbiology learns morphology, physiology, genetics and microorganisms systematization, their ecology and the other life forms. Specific Classes of Microorganisms Algae Protozoa Fungi (yeasts and molds) Bacteria Rickettsiae Viruses Prions The Microorganisms are extraordinarily widely spread in nature. They literally ubiquitous forward us from birth to our death. Daily, hourly we eat up thousands and thousands of microbes together with air, water, food. -
Biology 1015 General Biology Lab Taxonomy Handout
Biology 1015 General Biology Lab Taxonomy Handout Section 1: Introduction Taxonomy is the branch of science concerned with classification of organisms. This involves defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. Something that you will learn quickly is there is a lot of uncertainty and debate when it comes to taxonomy. It is important to remember that the system of classification is binomial. This means that the species name is made up of two names: one is the genus name and the other the specific epithet. These names are preferably italicized, or underlined. The scientific name for the human species is Homo sapiens. Homo is the genus name and sapiens is the trivial name meaning wise. For green beans or pinto beans, the scientific name is Phaseolus vulgaris where Phaseolus is the genus for beans and vulgaris means common. Sugar maple is Acer saccharum (saccharum means sugar or sweet), and bread or brewer's yeast is Saccharomyces cerevisiae (the fungus myces that uses sugar saccharum for making beer cerevisio). In taxonomy, we frequently use dichotomous keys. A dichotomous key is a tool for identifying organisms based on a series of choices between alternative characters. Taxonomy has been called "the world's oldest profession", and has likely been taking place as long as mankind has been able to communicate (Adam and Eve?). Over the years, taxonomy has changed. For example, Carl Linnaeus the most renowned taxonomist ever, established three kingdoms, namely Regnum Animale, Regnum Vegetabile and Regnum Lapideum (the Animal, Vegetable and Mineral Kingdoms, respectively). -
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. -
Genomic Sequence of 'Candidatus Liberibacter Solanacearum'
RESEARCH ARTICLE Genomic sequence of 'Candidatus Liberibacter solanacearum' haplotype C and its comparison with haplotype A and B genomes Jinhui Wang1*, Minna Haapalainen1, Thomas Schott2, Sarah M. Thompson3,4, Grant R. Smith3,4,5, Anne I. Nissinen6, Minna Pirhonen1 1 Department of Agricultural Sciences, FI-00014 University of Helsinki, Helsinki, Finland, 2 Herne Genomik, Neustadt, Germany, 3 The New Zealand Institute for Plant & Food Research Limited, Lincoln, New Zealand, 4 Plant Biosecurity Cooperative Research Centre, Canberra, ACT, Australia, 5 Better Border Biosecurity, a1111111111 Lincoln, New Zealand, 6 Management and Production of Renewable Resources, Natural Resources Institute a1111111111 Finland (Luke), Jokioinen, Finland a1111111111 a1111111111 * [email protected] a1111111111 Abstract Haplotypes A and B of `Candidatus Liberibacter solanacearum' (CLso) are associated with OPEN ACCESS diseases of solanaceous plants, especially Zebra chip disease of potato, and haplotypes C, Citation: Wang J, Haapalainen M, Schott T, D and E are associated with symptoms on apiaceous plants. To date, one complete genome Thompson SM, Smith GR, Nissinen AI, et al. of haplotype B and two high quality draft genomes of haplotype A have been obtained for (2017) Genomic sequence of 'Candidatus Liberibacter solanacearum' haplotype C and its these unculturable bacteria using metagenomics from the psyllid vector Bactericera cocker- comparison with haplotype A and B genomes. elli. Here, we present the first genomic sequences obtained for the carrot-associated CLso. PLoS ONE 12(2): e0171531. doi:10.1371/journal. These two genomic sequences of haplotype C, FIN114 (1.24 Mbp) and FIN111 (1.20 Mbp), pone.0171531 were obtained from carrot psyllids (Trioza apicalis) harboring CLso. -
Venatorbacter Cucullus Gen. Nov Sp. Nov a Novel Bacterial Predator
Venatorbacter Cucullus Gen. Nov Sp. Nov a Novel Bacterial Predator Ahmed Saeedi University of Nottingham Nicola Cummings University of Nottingham Denise McLean University of Nottingham Ian F. Connerton ( [email protected] ) University of Nottingham Phillippa L. Connerton University of Nottingham Research Article Keywords: Predatory bacteria, Campylobacter, Venatorbacter cucullus Posted Date: April 16th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-200707/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/22 Abstract A novel Gram-stain negative, aerobic, halotolerant, motile, rod-shaped, predatory bacterium ASxL5, was isolated from a bovine slurry tank in Nottinghamshire, UK using Campylobacter hyointestinalis as prey. Other Campylobacter species and members of the Enterobacteriaceae were subsequently found to serve as prey. Weak axenic growth on Brain Heart Infusion agar was achieved upon subculture without host cells. The optimal growth conditions were 37°C, at pH 7. Transmission electron microscopy revealed some highly unusual morphological characteristics related to prey availability. Phylogenetic analyses using 16s rRNA gene sequences showed that the isolate was related to members of the Oceanospirillaceae family but could not be classied clearly as a member of any known genus. Whole genome sequencing of ASxL5 conrmed the relationship to members the Oceanospirillaceae. Database searches revealed that several ASxL5 share 16s rRNA gene sequences with several uncultured bacteria from marine, and terrestrial surface and subsurface water. We propose that strain ASxL5 represents a novel species in a new genus. We propose the name Venatorbacter cucullus gen. nov., sp. nov. with ASxL5 as the type strain.