Taxonomy of Prokaryotes

474 Pages·2011·10.211 MB·1-473\474

by  Fred Rainey and Aharon Oren (Eds.)

Methods in Microbiology
Volume 38
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Methods in
Microbiology
Volume 38
Taxonomy of Prokaryotes
Edited by
Fred Rainey
Department of Biological Sciences,
Louisiana State University,
Baton Rouge,
LA, USA
and
Aharon Oren
Department of Plant & Environmental Sciences,
The Alexander Silberman Institute of Life Sciences,
The Hebrew University of Jerusalem,
Edmond Safra Campus Givat Ram,
Jerusalem, Israel
Amsterdam(cid:129)Boston(cid:129)Heidelberg(cid:129)London(cid:129)NewYork(cid:129)Oxford
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Dedication
(cid:1)
The editors dedicate this volume to the memory of Peter H.A. Sneath (1923 2011)
(cid:1)
and George A. Zavarzin (1933 2011) in recognition of their great contributions
to bacterial taxonomy.
Contents
s
t
n
e
Series Advisors.................................................................................................................................. ix t
n
o
C
List of Contributors.......................................................................................................................... xi
(cid:1)
1. Taxonomy of Prokaryotes Introduction.............................................................................. 1
Fred A. Rainey and Aharon Oren
2. How to Describe New Species of Prokaryotes...................................................................... 7
Fred A. Rainey
3. Phenotypic and Physiological Characterization Methods................................................. 15
Noel R. Krieg and Penelope J. Padgett
4. Microscopy................................................................................................................................. 61
Manfred Rohde
5. Peptidoglycan Structure........................................................................................................ 101
Peter Schumann
6. Cell Wall Teichoic Acids in the Taxonomy and Characterization of
Gram-positive Bacteria........................................................................................................... 131
Natal’ya V. Potekhina, Galina M. Streshinskaya, Elena M. Tul’skaya and
Alexander S. Shashkov
7. The Identification of Polar Lipids in Prokaryotes............................................................. 165
Milton S. da Costa, Luciana Albuquerque, M. Fernanda Nobre and Robin Wait
8. The Identification of Fatty Acids in Bacteria..................................................................... 183
Milton S. da Costa, Luciana Albuquerque, M. Fernanda Nobre and Robin Wait
9. The Extraction and Identification of Respiratory Lipoquinones of Prokaryotes
and Their Use in Taxonomy................................................................................................. 197
Milton S. da Costa, Luciana Albuquerque, M. Fernanda Nobre and Robin Wait
10. Detection and Characterization of Mycolic Acids and Their Use in
Taxonomy and Classification................................................................................................ 207
Atteyet-Alla Fetouh Yassin
11. Polyamines............................................................................................................................... 239
Hans-Ju¨rgen Busse
vii
12. Characterization of Pigments of Prokaryotes and Their Use in
Taxonomy and Classification................................................................................................ 261
Aharon Oren
13. Characterization of Prokaryotes Using MALDI-TOF Mass
Spectrometry............................................................................................................................ 283
B.Be´dis Dridi and Michel Drancourt
14. Determination of the G+C Content of Prokaryotes.......................................................... 299
Noha M. Mesbah, William B. Whitman and Mostafa Mesbah
(cid:1)
15. DNA DNA Hybridization................................................................................................... 325
Ramon Rossello´-Mo´ra, Mercedes Urdiain and Arantxa Lo´pez-Lo´pez
16. The Use of rRNA Gene Sequence Data in the Classification and Identification
of Prokaryotes.......................................................................................................................... 349
Wolfgang Ludwig, Frank Oliver Glo¨ckner and Pelin Yilmaz
17. Multilocus Sequence Determination and Analysis........................................................... 385
Paul De Vos
18. Whole Genome Sequence Comparisons in Taxonomy.................................................... 409
Rainer Borriss, Christian Rueckert, Jochen Blom, Oliver Bezuidt, Oleg Reva and
Hans-Peter Klenk
19. How to Name New Genera and Species of Prokaryotes?............................................... 437
Aharon Oren
Index................................................................................................................................................ 465
Colour Plate Section can be found at the back of this book
viii
Series Advisors
s
r
o
Gordon Dougan The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, vis
Cambridge CBIOISA, UK d
A
s
Graham J Boulnois Schroder Ventures Life Science Advisers (UK) Limited, 71 Kingsway, London e
ri
WC2B 6ST, UK e
S
Jim Prosser School of Medical Sciences, University of Aberdeen, Cruickshank Building, St Machar
Drive, Aberdeen,AB24 3UU, UK
Ian R Booth School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences,
Foresterhill,Aberdeen AB25 2ZD, UK
DavidAHodgsonDepartmentofBiologicalSciences,UniversityofWarwick,ConventryCV47AL,UK
David HBoxerUniversity of Dundee, Dundee DD1 4HN,UK
ix
List of Contributors
s
r
o
t
u
b
Luciana Albuquerque, Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, ri
Portugal nt
o
C
Oliver Bezuidt, University of Pretoria, Department of Biochemistry, Bioinformatics and
f
Computational Biology Unit, Pretoria, South Africa o
t
s
Jochen Blom, Centerfor Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany Li
RainerBorriss, ABiTEP GmbH, Berlin, Germany
Hans-Ju¨rgen Busse, Institut fu¨r Bakteriologie, Mykologie und Hygiene, Abteilung fu¨r Pathobiologie,
Veterina¨rmedizinische Universita¨t Wien, Wien, Austria
Milton S. da Costa,Departmentof Life Sciences,University of Coimbra, Coimbra, Portugal
Paul DeVos, Laboratory of Microbiology, GhentUniversity, Gent, Belgium
Michel Drancourt, Unite´ de Recherche sur les Maladies Infectieuses et Tropicales Emergentes UMR
CNRS 6236 IRD 198, IFR48, Institut Hospitalier Universitaire POLMIT, Universite´ de la
Me´diterrane´e,Marseille,France
B. Be´dis Dridi, Unite´ de Recherche sur les Maladies Infectieuses et Tropicales Emergentes UMR
CNRS 6236 IRD 198, IFR48, Institut Hospitalier Universitaire POLMIT, Universite´ de la
Me´diterrane´e,Marseille,France
Frank Oliver Glo¨ckner, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359
Bremen,Germany; Jacobs University Bremen GmbH, CampusRing 1, 28759 Bremen, Germany
Hans-Peter Klenk, DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig,
Germany
Noel R. Krieg, Departmentof Biological Sciences,VirginiaTech,Blacksburg,Virginia24061,USA
Arantxa Lo´pez-Lo´pez, Marine Microbiology Group, Department of Ecology and Marine Resources,
IMEDEA(CSIC-UIB), C/MiquelMarque´s21, E-07190 Esporles, Illes Balears, Spain
Wolfgang Ludwig, Lehrstuhl fu¨r Mikrobiologie, Technische Universita¨t Mu¨nchen, Am Hochanger 4,
85350 Freising, Germany
Mostafa Mesbah, Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University,
Ismailia 41522, Egypt
Noha M. Mesbah, Department of Biochemistry, Faculty of Pharmacy, Suez Canal University,
Ismailia 41522, Egypt
M. FernandaNobre, Department ofLifeSciences,University of Coimbra, Coimbra, Portugal
Aharon Oren, Department of Plant and Environmental Sciences, Institute of Life Sciences, and the
Moshe Shilo Minerva Center for Marine Biogeochemistry, The Hebrew University of Jerusalem,
Jerusalem 91904, Israel
xi
Penelope J. Padgett, Environment, Health & Safety, University of North Carolina, North Carolina
27599-1650, USA
Natal’yaV.Potekhina,Department of Biology,M. V.LomonosovMoscowStateUniversity,Moscow,
Russia
Fred A. Rainey, Department of Biological Sciences, Louisiana State University, Baton Rouge,
Louisiana 70803,USA
Oleg Reva, University of Pretoria, Department of Biochemistry, Bioinformatics and Computational
Biology Unit, Pretoria, South Africa
Manfred Rohde, Department of Medical Microbiology, Helmholtz Centre for Infection Research
(HZI),Braunschweig,Germany
Ramon Rossello´-Mo´ra, Marine Microbiology Group, Department of Ecology and Marine Resources,
IMEDEA(CSIC-UIB), C/MiquelMarque´s21, E-07190 Esporles, Illes Balears, Spain
Christian Rueckert, Center for Biotechnology(CeBiTec),Bielefeld University,Bielefeld, Germany
Peter Schumann, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und
Zellkulturen GmbH, Braunschweig, Germany
Alexander S. Shashkov, N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of
Sciences,Moscow, Russia
Galina M. Streshinskaya, Department of Biology, M. V. Lomonosov Moscow State University,
Moscow, Russia
Elena M. Tul’skaya, Department of Biology, M. V. Lomonosov Moscow State University, Moscow,
Russia
Mercedes Urdiain, Marine Microbiology Group, Department of Ecology and Marine Resources,
IMEDEA(CSIC-UIB), C/MiquelMarque´s21, E-07190 Esporles, Illes Balears, Spain
Robin Wait, KennedyInstitute of Rheumatology,Imperial College, London,United Kingdom
WilliamB. Whitman, Department ofMicrobiology,University ofGeorgia, Athens, GA 30602, USA
Atteyet-Alla Fetouh Yassin, Institut fu¨r Medizinische Mikrobiologie und Immunologie der
Universita¨t Bonn, Bonn, Germany
Pelin Yilmaz, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen,
Germany; Jacobs University Bremen GmbH, Campus Ring 1, 28759 Bremen, Germany
xii