Molecular Ecology of Denitrifiers Laurent Philippot
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Molecular ecology of denitrifiers Laurent Philippot To cite this version: Laurent Philippot. Molecular ecology of denitrifiers. Society for General Microbiology (SGM) Con- ference, Sep 2009, Edimbourg, United Kingdom. hal-01231278 HAL Id: hal-01231278 https://hal.archives-ouvertes.fr/hal-01231278 Submitted on 3 Jun 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. Microbiologysociety for general Autumn Meeting Edinburgh Conference Centre Heriot-Watt University 7–10 September 2009 e enc l sci obia g modern micr verin eli d PUTTING MICROBES TO WORK: the latest in translational and applied microbial science ABSTRACTS sgmconferencessociety for general microbiology Abstract Booklet Cover.indd 1 Poster modified for abs book cover.indd 1 28/07/200922/07/2009 15:56 11:26 CONTENTS SPONSORS ii DARWIN’S TREE OF LIFE HW01 1 PUTTING MICROBES TO WORK HW02 4 MICROBIAL POLYSACCHARIDES HW03 7 MICROBIAL FACTORIES HW04 10 ALTERNATIVE MODELS TO STUDY MAMMALIAN PATHOGENS HW07 12 CULTIVATING AND SENSING MICROBES IN MICRO-SCALE DEVICES HW08 14 GLYCOENGINEERING HW09 17 SIR HOWARD DALTON YOUNG MICROBIOLOGIST OF THE YEAR COMPETITION HW10 19 CONJUGATE VACCINES HW11 20 MICROBIAL STRESS AND FOOD PRODUCTION: COPING WITH THE WORK ENVIRONMENT HW12 23 BIOENERGY FUEL SOURCES HW13 25 POLAR MICROBIOLOGY HW14 28 BACTERIAL CELL WALLS HW16 31 CONTRIBUTION OF THE GLOBAL N CYCLE TO GLOBAL PROCESSES HW17 33 MENINGITIS (CLINICAL MICROBIOLOGY WORKSHOP) HW18 35 PRIZE LECTURES 37 FRED GRIFFITH REVIEW LECTURE MICROBIOLOGY OUTREACH PRIZE LECTURE POSTERS 38 AUTHORS 61 Please note: Abstracts are printed as received from the authors and are not subject to editing. www.sgmheriot-watt2009.org.uk – Contents i SPONSORS T he Society for General Microbiology would like to acknowledge the support of the following organizations and companies: Applikon Biotechnology Ltd www.applikon.co.uk Bioline www.bioline.com Broadley James Technologies Ltd www.broadleyjames.com Don Whitley Scientific Ltd www.dwscientific.co.uk GATC Biotech AG www.gatc-biotech.com Geneius Laboratories Ltd www.geneiuslabs.co.uk/ Synbiosis www.synbiosis.com Taylor & Francis Ltd www.tandf.co.uk Technopath www.techno-path.com Wellcome Trust Advanced Courses www.wellcome.ac.uk/advancedcourses Wisepress Ltd www.wisepress.com ii Sponsors – www.sgmheriot-watt2009.org.uk HW01 DARWIN’S TREE OF LIFE THE GREat TREE OF LIFE: FROM DARWIN TO bactERIAL DIVERSITY EVOLUTION OF THE MINIMALIST PLASTID GENOME OF DINOflagEllatES MARK J. PALLEN ADRIAN BARBrooK University of Birmingham, B15 2TT University of Cambridge, CB2 1QW The tree of life as a mythological concept is common to many cultures, ancient and Dinoflagellates possess an extremely reduced plastid genome relative to those examined modern. As a scientific metaphor for the evolutionary descent of organisms from common in plants and other algae. The organization of this genome is also radically different. ancestors, it is relatively modern, although several instances of its use predate Darwin – Analyses have revealed the genome reduction is the result of widespread transfer of most notably in Lamarck’s Philosophie Zoologique (1809). Early on, phylogenetic thinking also genes to the nucleus. The remaining genes mostly encode subunits of Photosystems I and II, the cytochrome b f complex, and ATP synthase, as well as rRNAs and a few tRNAs. In permeated disciplines outside biology, including historical linguistics and textual criticism. 6 Darwin left an iconic image of a phylogenetic tree in his B notebook from 1837–8. He typical plastid genomes all the genes are physically linked on a single molecule. However, included a phylogenetic tree as the only figure in The Origin of Species, where he also in dinoflagellates the plastid genes are located on small plasmids, commonly referred to as provides an eloquent description of ‘the great Tree of Life, which fills with its dead and ‘minicircles’. In the majority of cases a single gene is present on each minicircle, but examples broken branches the crust of the earth, and covers the surface with its ever branching and with up to four genes have been documented. A number of other unusual features are beautiful ramifications’.A lfred Russel Wallace also used this metaphor in his essay from associated with the dinoflagellate plastid genome, such as the presence of a region of high 1855 – ‘a complicated branching of the lines of affinity, as intricate as the twigs of a gnarled sequence identity on each minicircle, unusual codon usage, polyuridylylation of transcripts oak’ and is now buried under the trunk of a fossil tree. Darwin’s followers, particularly and the presence of ‘empty’ minicircles. We will discuss our current understanding of the German naturalist Ernst Haeckel, created more elaborate trees. However, rigour and a dinoflagellate genome and possible reasons for its evolution. measure of objectivity in tree building arrived only in the late twentieth century, with the advent of cladistics and molecular phylogenetics. Molecular biology has provided support A NEW ROOT FOR THE TREE OF LIFE for a common origin and ancestry of all living organisms. In recent decades, the tree of life JAMES LAKE metaphor has simultaneously been uplifted by wide-ranging and evermore sophisticated University of California at Los Angeles, USA surveys of biological diversity and downgraded by the discovery of rampant horizontal gene A rooted tree of life provides a framework to answer central questions about the evolution transfer in bacterial and archaeal genomes, twinned with doubts as to its applicability to the of life. Here we review progress on rooting the tree of life, and introduce a new root of life earliest stages of evolution. obtained through the analysis of indels, insertions and deletions, found within paralogous gene sets. Through the analysis of indels in 8 paralogous gene sets, the root is localized to VIRUS EVOLUTION: SYMBIOSIS, MUTUALISM AND SYMBIOGENESIS the branch between the clade consisting of the Actinobacteria and the double membrane MARILYN J. ROOSSINCK (Gram-negative) prokaryotes and one consisting of the archaebacteria and the Firmicutes. The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401, USA This root provides a new perspective on the habitats of early life, including the evolution Viruses are generally thought of as annoying pathogens, but that represents only a small of methanogenesis, membranes, hyperthermophily; and the speciation of major prokaryotic proportion of their lifestyle choices. If we think of viruses as symbionts, where they taxa. clearly belong in the original definition of symbiosis, we see that they can be mutualists Our analyses exclude methanogenesis as a primitive metabolism, in contrast to previous or antagonists, and are probably most often commensalists. Mutualistic viruses have only findings.T hey parsimoniously imply that the ether archaebacterial lipids are not primitive, and recently been studied, but they have dramatic effects on the survival of their hosts. We have that the cenancestral prokaryotic population consisted of organisms enclosed by a single, found that viruses can be instrumental in the rapid adaptation of their hosts to extreme ester-linked lipid membrane, covered by a peptidoglycan layer. These results explain the environmental shifts. This is because viruses may be a unique source of new genetic similarities previously noted by others between the lipid synthesis pathways in eubacteria information. This process has clearly happened throughout the evolution of life and the and archaebacteria. The new root also implies that the last common ancestor was not footprints of these events can be seen in the evidence of past viral integration into the hyperthermophilic, although moderate thermophily cannot be excluded. genomes of their hosts, a process of symbiogenesis. This presentation will discuss current discoveries of viral mutualistic symbiosis; evidence of the role of these events in the past; GRAFTING MITOCHONDRIA ONTO THE TREE OF LIFE and where viruses belong on the tree of life. MARK VAN DER GIEZEN Centre for Eukaryotic Evolutionary Microbiology, School of Biosciences, University of Exeter, THE NTH EUKARYOTIC ‘SUPERGRoup’ AND THE EVOLUTIONARY AND Exeter EX4 4QD ECOLOGIcal COMPLEXITY OF CERCOZOA DAVID BASS Eukaryotic life without mitochondria is unimaginable. It seems therefore quite amazing Dept of Zoology, Natural History Museum, London that these essential eukaryotic organelles are actually bacterial in origin. For years, the origin of the mitochondrial symbiont has been sought amongst the parasitic alphaproteobacteria Recently, developments in phylogenetic analyses have enabled significant advances towards such as Rickettsia. However, recent genomic and cell biological efforts aimed at resolving evolutionary relationships among protozoan lineages, which themselves represent understanding various protist lineages seem to underscore the notion that the bacterium a large proportion of the evolutionary history of eukaryotes including their earliest that gave rise to mitochondria