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Table of Contents
Table of Contents
Bacterial Systematics
N. A. LOGAN
1994
Blackwell Scientific
Publications
263 pp.
PowerPoints/pdf files/Monographs
Taxonomy
The Science of Classification
Taxonomy
1.
2.
3.
1. Identification
Basically, bacteria are identified/classified
according to phenotypic differences, or by
genotypic differences
10
11
2. Nomenclature
12
Bacterial nomenclature
Bull et al.,2008
14
15
1. The Code
1.
2.
3.
The Code
17
The Code
18
The Code
19
The Code
History
20
The Code
The Code
22
The Code
The Code
1990 Revision
The Code
1999 Revision
The Standards
27
The Standards
The Standards
The Standards
30
The Standards
The Standards
ISPP
34
Approved Lists
36
37
38
39
Bull et al.,2008
40
41
Legitimacy
Effectively Published/Validly
Published
Publishing unequivocally
proposed names in a journal or book that is readily
available (effective publication).
An effectively published name must be validly
published in IJSEM before it can be considered to
have a standing in nomenclature (Young,2008).
Validly Published: According to the Code, a proposed
name is validly published when the name appears in
IJSEM either as an original manuscript proposing the
name or through listing on the Validation Lists.
The Standards do not have a criterion for valid
publication.
Effectively Published:
44
Validation Lists
Valid publication
1.
2.
Validation Lists
Validation List
48
Validation Lists
Notification Lists
Notification Lists
Notification Lists
52
Notification List
53
Other codes
BioCode
54
The BioCode
Other codes
PhyloCode
The PhyloCode
Types of Clade
Official societies/committees on
taxonomy
ICSP
Judicial Commission
Ad Hoc Committee
58
Statutes of ICSB
59
i.
ii.
iii.
iv.
v.
61
2.
3.
62
(ii)
(iii)
(iv)
(v)
64
The Code
65
The Code
66
The Code
Principle 1
The essential points in nomenclature are as
follows:
Aim at stability of names,
Avoid or reject the use of names which may
cause error or confusion,
Avoid the useless creation of names.
67
The Code
Principle 2
According to Principle 2, the nomenclature of
Prokaryotes is not independent of botanical
and zoological nomenclature.
When naming new taxa in the rank of genus
or higher, due consideration is to be given to
avoiding names which are regulated by the
Zoological Code and the International Code of
Botanical Nomenclature.
68
The Code
Principle 3
The scientific names of all taxa are Latin or
latinized words treated as Latin regardless of
their origin.
They are usually taken from Latin or Greek.
69
The Code
The Rules:
Bull et al.,2008
70
The Code
The Code
Section 1. General
Rule 1a
This revision supersedes all previous editions of the International Code of
Nomenclature of Bacteria. It shall be cited as Bacteriological Code (1990
Revision) and will apply from the date of publication (1992).
Rule 1b
Alterations to this Code can only be made by the ICSB at one of its plenary
sessions. Proposals for modifications should be made to the Editorial Secretary in
sufficient time to allow publication in the IJSB before the next International
Congress of Bacteriology. For this and other Provisions, see the Statutes of the
ICSB, pp. 137 158.
Rule 2
The Rules of this Code are retroactive, except where exceptions are specified.
Rule 3
Names contrary to a Rule cannot be maintained, except that the International
Committee on Systematic Bacteriology, on the recommendation of the Judicial
Commission, may make exceptions to the Rules (see Rule 23a and the Statutes
of the ICSB).
Rule 4
In the absence of a relevant Rule or where the consequences of a Rule are
uncertain, a summary in which all pertinent facts are outlined should be
submitted to the Judicial Commission for consideration for preparation of a
Request for an Opinion).
72
The Code
The Code
74
Scientific Nomenclature
Binomial Nomenclature
Erwinia amylovora
75
Binomial nomenclature
The Swedish
naturalist, Carolus
Linneaus developed
a scientific system of
naming organisms.
Carolus Linnaeus (1707-1778)
76
Binomial nomenclature
S. scabies.
Scientific Names
Binomial Nomenclature
Scientific Binomial
Source of Specific
Epithet
The disease
P ectobacterium carotovorum
A pectolytic bacterium
carrot-devouring
Causes scab
Sphingos of sphinx
Erw inia
78
Binomial nomenclature
Valid names
Young,2008
79
The Code
The Recommendations
The Recommendation provide additional guidance, but in
contrast to the Rules are not obligatory.
It is recommended that names be reasonably short and easy to
pronounce (Recommendation 6).
Names may be chosen to recognize individual bacteriologists or
pathologists, but names honoring individuals quite unconnected
with bacteriology are discouraged (Recommendations 6, 10a,
12c).
For example, a novel species of Agrobacterium from Ficus
benjamina was proposed and named Agrobacterium larrymoorei
(of Larry Moore) to honor the renowned plant pathologist who
spent his career studying the genus Agrobacterium (Bouzar
and Jones, 2001).
Bull et al.,2008
80
Rejected names
81
Orthography of names
Contentious names
P hytoplasm a taxonomy
Candidatus status
85
Nomenclature
86
Nomenclature
Nomenclature
88
89
Minimal standards
90
Minimal standards
Minimal standards
Minimal standards
93
Minimal standards
94
Minimal standards
95
97
Minimal standards
98
99
Minimal standards
1.
2.
3.
4.
5.
100
Linnaean hiearchy
102
Linnaean hiearchy
Example:
Division: Gracilicutes
Class: Scotobacteria
Family: Enterobacteriaceae
Genus: Erwinia
Species: amylovora
Karlm,2004
103
Linnaean hiearchy
Levels of Classification
104
Nomenclature of strains
Nomenclature of
Infrasubspecific Taxa
106
107
108
Suffixes
Suffixe
Subtribe
-inae
Tribe*
-eae
Subfamily
-oideae
Family
-aceae
Suborder
-ineae
Order
-ales
Subclass
Class
Division or phylum**
Domain or empire**
*Taxonomic category not in current use; ** Taxonomic category not covered by the Rules.
109
Jackson,2009
110
111
112
Bergey's Manuals
Morphology, differential
staining, biochemical tests
DSMZ
115
116
List of
Prokaryotic names
With Standing in
Nomenclature
117
118
Bull et al.,2008
121
122
123
Dan Opgenorth,2005
124
Synonyms
Agrobacterium rhizogenes
Rhizobium rhizogenes
Agrobacterium rubi
Rhizobium rubi
Corynebacterium fascians
Rhodococcus fascians
Corynebacterium m ichiganense
Pectobacterium carotovorum
Brenneria nigirfluens
Burkholderia caryophylli
Ralstonia solanacearum
125
127
Searching and
ordering strains
from NCPPB
Culture
Collection
128
Searching and
ordering strains
from NCPPB
Culture
Collection
129
CFBP
Portier,2009
130
CFBP
Conservation facilities
Portier,2009
131
CFBP
Deposit of strains
132
CFBP
Strain ordering
Portier,2009
133
DSMZ
134
Material transfer
Trudy Wassenaar,2007
136
Museum of Bacteria
Information on bacteria
137
3. Classification
Classifications group similar things together
138
Prokaryotes
The History
1735
1857
1866
1937
1961
1959
1968
1978
139
Prokaryotes
Karlm,2004
140
143
Classification systems
Two general ways to classify based on:
Overall similarity phenetic
Evolutionary relationships phylogenetic
Therefore:
Taxonomy is traditionaly phenotypic.
Phylogeny is mainly genetic.
144
145
Phylogenetic system
Phenetic system
146
1. Phenetic Classification
Classical (Numerical taxonomy)
Numerical taxonomy is a common approach to phenetic taxonomy
147
Phenetic Classification
148
Two kingdoms
151
Kingdom Monera
Classification of Bacteria
Classification of Bacteria
Phylum Gracilicutes
Class Scotobacteria
Order Spirochaetales
Order Pseudomonadales
Order Rickettsiales
Order Chlamydiales
Class Anoxyphotobacteria
Class Oxyphotobacteria
Phylum Firmicutes
Class Firmibacteria
Class Thallobacteria
Order Actinomycetales
Phylum Tenericutes
Class Mollicutes
Phylum Mendosicutes
Class Archaebacteria
152
2. Phylogenetic Classification
Systematics is divided primarily into
phylogenetics and taxonomy
153
Phylogenetics
154
155
156
157
Eucarya
Bacteria
70S
80S
70S
Methionine
Methionine
Formylmethionine
Introns in tRNA
Yes
Yes
No
Membrane lipids
Ether-linked
Ester-linked
Ester-linked
NO
NO
Yes
Kanamycin
NO
NO
Yes
Streptomycin
NO
NO
Yes
Rifampicin
NO
NO
Yes
Characteristic
Ribosomes
Initiator tRNA
Sensitivity to:
Choramphenicol
158
159
1.
2.
3.
Seelke,2010
161
1.
2.
3.
4.
164
A. Phenetic Classification
Conventional Bacterial Taxonomy
(Numerical taxonomy)
165
Numerical Taxonomy
Phenetic Taxonomy
Logan,1994
167
Classical characteristics
168
Cellular components
and methods in
chemotaxonomy
Logan,1994
169
Numerical Taxonomy
Phenetic Taxonomy
170
Numerical Taxonomy
Relies on similarity coefficients.
Calculates the percentage of characteristics
that two organisms or groups have in
common.
If use 10 characteristics, then match
organisms:
Example:
A and B share 8 characters out of 10: similarity coefficient Sab is
8/10=0.8 (80%). Can use many such values to establish similarity
matrix. Dendrograms help display this information clearly.
171
Similarity coefficient
Usually expressed in percent
Similarity coefficient
Numerical Taxonomy
Greater similarity coefficient,
closer relatedness is inferred.
Greater than ~70% and inference
is that two compared bacteria are
of the same species.
174
Numerical taxonomy
175
Computer assisted
identification database
176
Numerical taxonomy
Arange the
coeficients for
matches between
very many
organisms by
computer into a
matrix (similarity
matrix) -->
177
Numerical taxonomy
Dendogram
Dendrogram of
phenotypic
characteristics strains
of phytopathogenic
Enterobacteriaceae
179
B. Polyphasic Taxonomy
A Consensus Approach to Bacterial Systematics
180
The development of
prokaryote taxonomy
The development of
prokaryote taxonomy
The development of
prokaryote taxonomy
Polyphasic taxonomy
184
185
Polyphasic Taxonomy
Taxonomy is generally taken as a synonym of systematics or
biosystematics and is traditionally divided into three parts:
i.
Classification: The orderly arrangement of organisms into
taxonomic groups on the basis of similarity,
ii.
Nomenclature: The labelling of the units defined in (i),
iii.
Identification: The process of determining whether an
organism belongs to one of the units defined in (i) and labeled
in (ii).
187
Characteristics used in
polyphasic taxonomy
Phenotypic Methods
Classical phenotypic analyses
Numerical analysis
Automated systems
Genotypic Methods
Determination of the DNA base ratio (moles percent GC)
DNA-DNA hybridization(DDH) studies
rRNA homology studies (Ribotyping: molecular fingerprinting)
DNA-based typing methods
Typing methods
Cell wall composition
Cellular fatty acids
Isoprenoid quinones
Whole-cell protein analysis
Polyamines
Siderotyping is a new determinative tool for accurate identification of
pseudomonads at the species level(Meyer et al ., 2002).
188
G+C
Mol% (G + C) =
100%
G+C+A+T
189
Classification
191
Classification
Based on DNA
homology
Classification of Acidovorax
Based on DNADNA hybridization
193
194
Polyphasic
taxonomy
Taxonomic
resolution of some
of the currently
used techniques
Vandamme et al.,1996
195
196
198
199
16S rRNA
Karlm,2004
202
203
Polyphasic approach
Based on 16S23S rDNA ITS
Pseudomonas.
Polyphasic approach
Based on 16S23S rDNA ITS
205
PCR-RFLP
206
PCR-RFLP analysis
Detecting rRNA molecules
207
Polyphasic approach
208
Polyphasic approach
Based on gyrB ,rpoD,.. genes
Polyphasic approach
Neil Parkinson
211
Polyphasic approach
Based on recA gene
212
Polyphasic approach
Based on recA gene
Lojkowska et al.,2004
213
Polyphasic approach
Based on recA gene
Lojkowska et al.,2004
214
Polyphasic approach
Based on recA gene
Lojkowska et al.,2004
215
Polyphasic approach
Based on recA gene
Lojkowska et al.,2004
216
Polyphasic approach
Based on rpoS gene
Lojkowska et al.,2004
217
Polyphasic approach
Based on rpoS gene
Lojkowska et al.,2004
218
Polyphasic approach
Based on rpoS gene
Lojkowska et al.,2004
219
Polyphasic approach
Based on rpoS gene
Lojkowska et al.,2004
220
Polyphasic approach
Based on gyrA gene
Lojkowska et al.,2004
221
Polyphasic approach
Based on gyrA gene
Lojkowska et al.,2004
222
Polyphasic approach
Based on gyrA gene
Lojkowska et al.,2004
223
Polyphasic approach
Based on gyrA gene
Lojkowska et al.,2004
224
Polyphasic approach
Based on gyrA gene
Lojkowska et al.,2004
225
Polyphasic approach
Pectolytic enterobacteria
Based on recA gene
recA pectolytic
enterobacteria
lineages
Neil Parkinson
226
Polyphasic approach
227
Polyphasic approach
P seudom onas
Neil Parkinson
228
Injection apparatus,
together with effector
proteins,for parasitising
euckaryotic cells.
Required for by
proteobacteria to
produce infection of
plants and animals.
Required for
colonization and plant
defence activation in
growth promoting
strains.
Neil Parkinson
229
Neil Parkinson
230
P. syringae
phylogeny using
gyrB
Neil Parkinson
231
Polyphasic approach
Classification of pseudomonads
MLST is a highly
discriminating, rapid, and
portable DNA-based strain
typing method in which
regions from several
housekeeping loci are
sequenced from each strain.
A preliminary multilocus
sequence typing (MLST)
analysis of 367 strains within
the genus Pseudomonas
identified major clades
corresponding to P. syringae,
P. viridiflava, P. fluorescens,
P. putida, P. aeruginosa, and
P. stutzeri.
Guttman et al.,2008; David Stead
232
Classification of pseudomonads
Classification of pseudomonads
The MLST primers: Used for DNA amplification and
sequencing of the four loci
Guttman et al.,2008
234
Multilocus sequence
typing (MLST)
analysis
Guttman et al.,2008
235
P . syringae phylogeny
Based on Multilocus sequence
typing (MLST) analysis (Seven
locus mlst).
(Courtesy Sarker and Guttman)
Neil Parkinson
236
Polyphasic approach
X anthom onas
Xanthom onas
species
identification using
gyrB
Parkinson,2007
237
Xanthom onas
Polyphasic approach
Based on gyrB gene
New xanthomonad
species-level
clades identified
using gyrB .
Neil Parkinson
238
Polyphasic approach
Based on lrp gene
239
Polyphasic approach
Based on lrp gene
Phylogeny based on
Leucine responsive
regulatory protein
(LR P ) analysis
A dendrogram based on
pairwise comparison of all
lrp sequences showed that
Xanthomonas species
grouped together, with P.
aeruginosa and R.
solanacearum as
outgroups.
The largest cluster within
Xanthomonas was cluster
1 which encompassed all
strains that are presently
proposed as pathovars of
X. axonopodis (Vauterin et
al.,2000).
Cubero & Graham,2003
241
Siderotyping
A Powerful Tool for the Identification of
Fluorescent and Non-fluorescent Pseudomonads
242
Siderotyping
Phenotypic characterization
Pseudomonas reactans.
243
Iron acquisition
Iron acquisition
245
Siderotyping
247
Schalk ,I.S.2006. Pseudomonas, Volume 4, Ramos, JuanLuis and Roger, C. Levesque (Eds.).
248
249
Siderophore types
250
251
252
254
An example of a pyoverdine
Quinoline chromophore:
Imparts the color and fluorescence to the molecule. Its
catechol unit is one of the binding sites for iron (III).
Peptide chain:
Peptide chain contains L-, D-, and uncommon amino acids.
The amino acids of the peptide chain, or some of them,
should be responsible for the recognition of the ferripyoverdine molecule at the outer membrane receptor
protein, which is strain-specific.
Acyl side chain:
Unlike the both parts of the molecule i.e. chromophore &
peptide chain which participate in the complexation of the
iron(III) ion, the nature of the acyl chain does not affect
iron transport.
258
Chromophore types
Chromophore types that are produced along with the one of pyoverdine.
259
Siderovars regroup
strains that produce
pyoverdins with the
same peptide chain.
260
261
Purification of pyoverdins
General method
Siderotyping methods
264
265
IEF patterns
266
PVD-IEF patterns
267
Pyoverdine isoelectric
focusing profile
Isoelectrophoretic patterns of
pyoverdines produced by:
lane 1, P. putida strain C; lane 2,
P. putida ATCC 12633; lane 3, P.
fluorescens strain ii; lane 4, P.
rhodesiae CFML 92-104; lane 5,
P. aeruginosa ATCC 15692; lane
6, P. fluorescens strain 1.3.
Lane 7 represents the
isoelectrophoretic pattern of an
equal mix of the pyoverdines
depicted in lanes 1 to 6 which
could be used as an internal
standard for pyoverdine
isoelectrophoretic pH (pI)
determination.
The pI values indicated on the
left side were determined by the
gel slicing method.
268
270
pI values of PVDs of P .
tolaasii and P .
reactans strains and
grouping of the strains
into siderovars
271
Cross Uptake
273
Neil Parkinson
274
Definition of species
The basic unit of taxonomy
275
Definition of species
Definition of species
Strain:
A population of microbes descended from a single
individual or pure culture.
Different strains represent genetic variability within a
species:
Biovars: Strains that differ in biochemical or
physiological differences.
Morphovars: Strains that vary in morphology.
Serovars: Stains that vary in their antigenic
properties.
Hendrix, J.D. 2004
277
Taxomomy, Pdf.,2004
278
Species concept
Some more problems
279
Species concept
1.
2.
3.
4.
5.
6.
7.
Microbial diversity
Types of diversity
Morphological diversity:
Bacilli, cocci, and spirals are 3 common shapes, but we've also
seen filamentous forms, pleiomorphic forms. Although most
bacteria are tiny, there are many varieties of size, ranging from
submicroscopic up to a few bacteria that can be seen with the
naked eye.
Structural diversity:
There are major differences between gram-positive and gramnegative bacteria, and even more profound structural
differences between bacteria and archaea.
Other differences include presence or absence of walls, external
appendages (capsules,..), endospores, etc.
281
Microbial diversity
Types of diversity
Metabolic diversity:
Heterotrophs vs autotrophs.
We have seen major differences between the metabolic needs
of heterotrophic and autotrophic microorganisms, and between
catabolic styles such as fermentation vs respiration (aerobic and
anaerobic).
Genetic diversity:
Small ribosomal subunit sequencing has profoundly altered our
perception of the extent of genetic diversity.
Now that genomes are being sequenced for many microbes, the
full extent of this diversity is being understood as never before.
The great bulk of life's diversity is not in the eukaryotes, but in
the bacteria and archaea.
282
Prokaryotic genome
283
Flexible genome
Non-essential
Variable
Can be weak
Neil Parkinson
285
Prokaryotic genome
Gene loss and acquisition
288
Bacterial Speciation
Gene flow
289
Species concept
290
Species concept
291
293
Allopatric/Sympatric/
Platypatric Speciation
Allopatric Speciation:
Sympatric Speciation:
294
Transduction,
Transformation,
Conjugation.
296
Species concept
297
Transformation
298
Comparison of
299
Conjugation
Conjugative plasmids
Conjugative plasmids
Mediators of DNA transfer
302
303
Collins Johnson
304
305
Conjugative plasmids
Mediators of DNA transfer
307
Species discovery
Exploring biodiversity
During the last years, the number of new isolates as well as the amount
of information useful for systematics has increased significantly. New
309
combinations of already existing taxa have not been included.
Polyphasic approach
Taxomomy,Pdf.2004
311
Taxomomy,Pdf.2004
312
Taxomomy,Pdf.2004
314
Taxomomy,Pdf.2004
315
Taxomomy,Pdf.2004
317
318
320
Taxomomy,Pdf.2004
321
Ribosomal RNAs
i.
ii.
iii.
iv.
324
326
Species concept
using 16S rRNA
sequences
Goal
Learn and understand the steps necessary to make a
phylogenetic assignment for a nucleotide sequence (here the
bacterial 16S rDNA).
Background
The nucleotide sequence of extracted nucleic acid can be
compared with a database of already assigned sequences.
330
DNA sequencing
rDNA
331
DNA sequencing
rDNA
332
DNA sequencing
rDNA
333
DNA sequencing
334
7.
8.
9.
Extract nucleic acid from isolates or amplify sequence in the polymerase chain
reaction.
Purify pure culture or amplified DNA using a kit.
Send to sequencing facility for PCR based sequencing with an appropriate
primer.
Edit sequence.
Using the web based database (The Ribosomal Database Project (RDP) find
closest relative to the primary structure of this sequence with Sequence Match.
Align sequences with aligned sequences of the closest relatives from the RDP
database using alignment software. Proof read the alignment: base the
alignment of conserved and variable areas on secondary structure of a closely
related organism (available from your instructor or specified web pages.
Create a distance matrix.
Test sequence for potential chimeric structures.
Export the aligned product and the aligned sequences of the closest relatives
into software able to create a tree of phylogenetic relationship based on specific
algorhythms.
Now enough is known to design a probe for the analyzed sequence.
Microbial ecology (BIOL4365),1999
335
MicroSeq
A.
B.
C.
D.
E.
Tang et al.,1998
337
3.
4.
5.
338
Moran,2010
341
Moran,2010
342
NCBI
343
NCBI
www.ncbi.nlm.nih.gov/blast
EBI
www.ebi.ac.uk/blast
EMBNet www.expasy.ch/blast
Moran,2010
346
How to align
Running BLAST
BLAST
349
Graphic Display
Hit List
Overview of the
alignments
Alignments
353
354
Description
E-Value
Bit score
Links
Genome
Uniref, database of
transcripts
Spiegel,2007
Moran,2010
356
357
Partial 16S rDNA sequence alignment of 13 Xanthomonas and Stenotrophomonas typestrains and seven X. translucens pv. graminis (X.t.g.) isolates.
Shading indicates sequence differences to the X.t.g. type-strain.
Bars mark the diagnostic PCR primer site characteristic for the X.t.g. group.
Numbers on top denote position in the E. coli reference sequence.
Klliker et al.,2006
Software analysis
Software analysis
PHYLIP
Version 3.6
Neighbor-joining analysis of
DNA sequences from several
Enterobacter spp.
Phylogenetic analysis was based
on full 16S rRNA gene
sequences, and the scale
reflects relative phylogenetic
distance.
Isolates with names beginning
with Mayo were evaluated in
this study.
Isolates with names beginning
with accession numbers were
retrieved from GenBank.
The remaining isolates, whose
names begin with ATCC
numbers, were type strains
stored in the MicroSeq
database.
Tang et al.,1998
362
Janse,2006
364
By adding your new sequence to the existing databases, scientists that discover
similar 16S rRNA sequences in the future will be able to find out about your
bacterium, as well as the habitat and environmental conditions under which your
bacterium was isolated.
To submit your sequences use a web browser to go to the GenBank entry page
at http://www.ncbi.nlm.nih.gov/BankIt.
Scroll down the page until you see the section shown in next Fig. showing
Portion of the GenBank submission page showing how to enter the BankIt page.
Enter the number of nucleotides in your trimmed sequence in the box and click
the 'New' button.
Moran,2010
365
The web page that appears next is a BankIt entry form that assigns a unique
number to your entry. Scroll down through the form, entering information
exactly as shown in the appendix.
After youve finished filling in the BankIt form, click the Validate and Continue
button at the bottom.
A series of pages will appear asking you to check for possible errors. Ignore the
warning message about not providing a recognized organism name (your isolate
doesn't have a one); just scroll to the bottom of the form and click 'Validate and
Continue' again. When asked if you want to modify your submission regarding
coding regions or other featuers, don't make any changes; select 'Submit to
Genbank'. And when asked if you forgot to indicate a coding sequence interval
in your submission, say you didn't (your gene doesn't code for a protein). Read
these error pages carefully to make sure your submission isn't cancelled without
you knowing it.
Moran,2010
366
1.
2.
3.
When you the get to the final Thank you for using
Bankit page (see what it looks like in the Appendix),
your submission is complete.
GenBank will contact you by e-mail to:
Give you a copy of your submission,
Give you the GenBank submission number assigned
to your sequence, and
Show you your final submission after GenBank staff
have checked/corrected the format.
Moran,2010
367
369
Species boundaries
Correlation between
RBR (relative binding
ratio) and Tm values.
Commonly accepted
values for species
boundaries are
indicated in green.
370
Species concept
Species concept
372
Species concept
Species concept
375
Xanthom onas
These tRNAs were highly conserved and divided the ITS sequence into three
regions (ITS1, ITS2 and ITS3).
Most Xanthomonas species had a shorter sequence nt (named ITS2-S), but five
species exhibited a longer sequence, of 78-85 bases (ITS2-L) caused either by:
The addition of a long stretch of 51-56 nt and two smaller (CCT and GCACA)
sequences, or by
The loss of these sequences from the other species.
376
377
Protein trees
More-reliable results are likely to be obtained if both
16S rRNA and rpoB genes are sequenced.
The rpoB gene, which encodes the beta-subunit of
bacterial RNA polymerase (protein), has been used
for species delineation and identification of numerous
genera, including mycobacteria.
The entire sequence of the 16S rRNA (1,500 bp) or
rpoB gene (4,000 to 4,500 bp) containing <1%
undetermined positions would be required for the
description of a new taxon.
381
Terminology
Terminology
Genospecies/genomospecies/genomic species
383
Terminology
Genospecies/genomospecies/genomic species
Genomospecies (genospecies):
The phylogenetic definition of a species (genomospecies) generally
would include strains with approximatively 70% or greater DNA-DNA
relatedness.
Change in rank
All strains clustered in these six genomic species( genomospecies 1-6)
be assigned to the six species:
Dickeya zeae sp. nov.
Dickeya dadantii sp. nov.
Dickeya chrysanthemi comb. nov.
Dickeya dieffenbachiae sp. nov.
Dickeya dianthicola sp. nov.
Dickeya paradisiaca comb. nov., respectively.
384
Terminology
385
Terminology
Terminology
387
Terminology
Terminology
Selected References
Selected References
Selected References
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