Lesson 2B: (SPECIES CONCEPT AND TAXONOMIC METHODS) Flashcards
1
Q
Species concept
A
Species are the fundamental units of biological diversity, and how we distinguish
and classify species in microbiology greatly affects our ability to explain and assess
the diversity of the microbial world. At present, there is no universally accepted
concept of a microbial species. Microbial systematics combines phenotypic,
genotypic, and sequence-based phylogenetic data within a framework of standards and guidelines for describing and identifying microorganisms in a taxonomic framework, but the issue of what actually constitutes a species remains
controversial. However, a working definition of a microbial species has been
developed and widely used
2
Q
should be genetically and
phenotypically cohesive, i.e. , they share distinct traits
that are unique only to the species.
A
Members of a species
3
Q
A species should also be what
A
monophyletic
4
Q
strains composing the species should all share a recent
common ancestor to the exclusion of other species
A
Monophyletic
5
Q
What do the species concept require
A
requires that a majority of genes in the species have
congruent phylogenies and share a recent common ancestor.
6
Q
Phylogenetic species concept is not based on
A
evolutionary model of speciation, and thus species described in this
way do not necessarily reflect meaningful units in terms of ecological or
evolutionary processes
7
Q
developed to
facilitate taxonomy
A
Phylogenetic species concept
8
Q
species justifications derived from this concept are
based largely on what
A
Expert judgement of taxonomists
9
Q
Phylogenetic species concept
A
a
species is a group of strains that share certain
characteristic traits and which are genetically
cohesive and share a unique recent common
ancestor.
10
Q
are defined
operationally as a group of strains sharing a high
degree of similarity in many traits and sharing a recent
common ancestor for their SSU rRNA genes.
A
Species of Bacteria and Archaea
11
Q
species of Bacteria and Archaea shares a what
A
- high
degree of similarity in many traits - share a recent
common ancestor for their SSU rRNA genes
12
Q
What approach die the species characterization employ
A
polyphasic approach
13
Q
What js polyphasic approach
A
considers a range of different traits in making taxonomic
judgments
14
Q
Traits currently considered most important for
identifying species
A
genomic similarity based on DNA
hybridization and comparisons of SSU rRNA sequences.
15
Q
provides a measure of
their genomic similarity.
A
degree of DNA–DNA hybridization
16
Q
GENOMIC HYBRIDIZATION: is isolated from the organisms
to be compared and then sheared and
denatured
A
Genomic DNA
17
Q
GENOMIC HYBRIDIZATION: is prepared from
organism 1 by shearing, denaturing, and
labeling the DNA
A
Probe DNA
18
Q
How is probe DNA prepared
A
shearing, denaturing, and
labeling the DNA
19
Q
GENOMIC HYBRIDIZATION: immobilized on a membrane
and then hybridized with the labeled probe DNA
from organism 1
A
Sheared single-stranded target DNA from
each genome
20
Q
is measured in genomic hybridization
A
Radioactivity in the hybridized
DNA
21
Q
is taken as the 100%
hybridization value.
A
Radioactivity in the control (organism 1 DNA
hybridizing to itself)
22
Q
( %) is taken as evidence that the two are distinct species.
A
A value of 70% or less genomic hybridization and a difference in SSU rRNA gene sequence
of 3% or more between two organisms
23
Q
suggest that these criteria are valid, reliable, and consistent in
identifying new microbial species for taxonomic purposes
A
experimental data
24
Q
Pairs of microorganisms are compared on what basis
A
16S rRNA similarities and
DNA–DNA hybridization values.
25
are likely
members of the same species
Points in the
upper right region represent pairs of strains
that share greater than 97% 16S rRNA gene
sequence similarity and 70% genomic
hybridization values
26
On the basis of this phylogenetic species concept, over how many species of Bacteria and Archaea have been
formally recognized.
10,000
27
discrete genera typically have how many % dissimilarity in their SSU rRNA gene sequences.
Greater than 5%
28
There are no consensus criteria for what
defining taxonomic ranks above the level of genera.
29
Eukaryotic species = ?
interbreeding populations.
30
microbes are ___
asexual
31
how many percent of the microbes are DNA hybridization
>70%
32
how many % of rRNA sequence identity of the microbes is considered part of the same sp.
>97%
33
why is there no firm estimate of the number of bacterial and archaeal
species can be given at present
because of uncertainty
about what defines a species in these domains. But this
number is expected to be very large
34
indicate that over 10,000
different species can coexist in a single gram of soil
Analyses of environmental SSU rRNA gene sequences using the
phylogenetic species concept
35
Since 1977 how many SSU rRNA sequences have
been generated and used to characterize the vast diversity of
the microbial world
3.3 million
36
contains an ever-growing collection
of SSU rRNA sequences and provides computational programs for their analysis and for the construction of phylogenetic trees.
The Ribosomal Database Project (RDP)
37
RDP provides what
quality-controlled, aligned and annotated Bacterial and Archaeal 16S rRNA sequences
- Fungal 28S rRNA sequences
-a suite of analysis tools to the scientific community.
38
how to construct evolutionary relationship
1. observe
2. biological records
- fossils
-geology
3. infer from the data of current organism (chemistry, gene sequence, protein sequence)
39
T or F: all of organisms in the tree of life are ancient
F - all are modern organism
40
T or F: some organisms in the tree of life may have characteristics of ancient organism
T
41
What does the polyphasic approach use
many different methods in combination
42
polyphasic approach is used to identify what
to identify and name species of Bacteria and Archaea
in
accordance with the currently accepted
phylogenetic species concept
43
we describe
methods commonly used for what
characterizing
microbial, and primarily prokaryotic, species.
44
Gene sequences are commonly determined from what
PCR-amplified
fragments of DNA, and the sequences are analyzed using
phylogenetic analyses.
45
- highly conserved
- while they provide valuable phylogenetic information, they are not always useful for distinguishing closely related species.
SSU rRNA gene sequences
46
Other highly conserved genes that can be useful for distinguishing bacteria at the species level
recA
gyrB
47
encodes a
recombinase protein
recA
48
encodes DNA gyrase
gyrB
49
accumulate
mutations more rapidly than rRNA genes
DNA sequences of protein-encoding genes
50
what species do the DNA sequences of protein-encoding genes can often distinguish that cannot be resolved by rRNA gene
sequence analyses alone.
prokaryotic species
51
is a method that uses “housekeeping “genes from several
related organisms , which are sequenced and the sequences used
collectively to distinguish the organisms.
Multilocus sequence typing (MLST)
52
encode essential functions in cells and are
always located on the chromosome rather than on a plasmid.
housekeeping genes
53
where are housekeeping genes always located
chromosome
54
In MLST, how many base-pair sequence is amplified and then sequenced for each gene
approximately 450-base-pair sequence
55
STEPS in MLST
isolate DNA -> Amplify 6-7 target genes -> sequence -> analyze allele then, compare w/ other strains and generate tree
56
a rapid approach for evaluating polymorphisms between strains of a species.
genome fingerprinting
57
genome fingerprints are generally
what
fragments of DNA generated from individual genes or whole genomes.
58
example of genome fingerprinting
ribotyping
59
a form of genome fingerprinting based on the localization of SSU rRNA genes on genome fragments
ribotyping
60
ribotyping is based on what
localization of SSU rRNA genes on
genome fragments
61
Genome fingerprinting method: ribotyping
genomic DNA from an organism is digested by a restriction enzyme and the fragments are separated by gel electrophoresis, transferred to a nylon membrane, and labeled with an SSU rRNA gene probe
62
ribotyping results
4 different lactic acid bacteria
63
Different microbial species can have different numbers of what
rRNA operon
64
rRNA operons can range from
1 - 15
65
is a conserved feature of all strains of a species
the number of
rRNA operons present in a microbial genome
66
Changes in genome sequence between strains
can cause the
endonuclease enzyme to cut in different locations, producing
variation in the lengths of the restriction fragments that are
visualized
67
generates a
specific pattern
size and number of bands
68
- a specific pattern generated by size and number of bands
- kind of genome fingerprint
- can be compared with patterns of reference organisms
in a computer database.
ribotype
69
The ribotype of a particular organism can be
unique and
diagnostic, allowing rapid identification of different species
and even different strains of a species
70
Other common genome
fingerprinting methods
1. repetitive extragenic palindromic
PCR (rep-PCR)
2. amplified fragment length polymorphism (AFLP)
71
based on the
presence of highly conserved repetitive
DNA elements interspersed randomly
around the bacterial chromosome.
rep-PCR method
72
The number and positions of these
elements differ between strains of a
species.
DNA elements
73
Genomic DNAs from five strains (1–5) of a single species of bacteria were PCR-amplified using specific primers called
rep (repetitive extragenic
palindromic)
74
were
separated in an agarose gel on the
basis of size to generate DNA
fingerprints.
PCR Products
75
where is PCR products separated
agarose gel
76
what is the basis of the separation of RNA products
size to generate DNA
fingerprints.
77
is based on the digestion of genomic DNA with one
or two restriction enzymes and selective PCR amplification
of the resulting fragments
amplified fragment length polymorphism (AFLP).
78
WHERE is AFLP based on
digestion of genomic DNA with one
or two restriction enzymes and selective PCR amplification
of the resulting fragments
79
what is generated in AFLP
Strain-specific banding
patterns similar to those of rep-PCR or other DNA
fingerprinting methods
80
AFLP: giving a high degree of discrimination
between strains within a species.
LARGE NUMBER OF BANDS
81
becoming increasingly common as
DNA sequencing capacities improve and costs decline.
use of multiple genes and entire genomes for the identification
and description of bacteria
82
wide range of sequence analyses can be performed on what
entire
genomes
83
what does sequence analyses on entire genomes provide
- insights into microbial physiology and microbial evolution.
- large role that horizontal gene exchange has played in
microbial evolution and on the highly dynamic nature of microbial
genomes
84
Shared orthologs can be
aligned and examined using
phylogenetic methods
85
what is determined in shared orthologs that is examined using phylogenetic methods
average nucleotide identity of these genes
86
provide further
insights into relationships between strains.
Comparative analyses of gene content (presence or absence of genes), synteny
(the order of genes in the genome), and genome GC content)
87
Entire genome sequences can also
be used for
metabolic reconstruction and characterization of a cell’s genetic
capacities
88
have been developed for use in systematic analyses
Several methods in comparative genomics and population genomics
89
provide many traits that
can be used to differentiate species
phenotype of a bacterium
90
are determined routinely when
describing a new microorganism.
phenotypic traits
91
compared to the phenotypes of organisms that
have been described previously.
phenotypic results
92
The phenotypic traits that are determined will depend on what
type
of organism being described.
93
General categories of some phenotypic traits used in identification and species description
-morphology
- motility
- metabolism
-physiology
- cell lipid chemistry
- cell wall chemisrty
- other traits
94
class/example of fatty acids in bacteria
1. saturated
2. unsaturated
3. cyclopropane
4. branched
5. hydroxy
95
saturated
tetradecanoic acid
96
unsaturated
omega-7-cis hexadecanoic acid
97
cyclopropane
cis-7,8-methylene hexadecanoic acid
98
branched
13-methyltetradecanoic acid
99
hydroxy
3-hydroxytetradecanoic acid
100
method used to identify these
fatty acids; widely used in
clinical, public health, and food-
and water inspection laboratories
where pathogens routinely must
be identified
FAME (fatty acid methyl ester):
101
varies from
species to species in chain length
and in the presence or absence
of double bonds, rings, branched
chains, or hydroxy groups
Fatty acid composition of
Bacteria (domain)
102
Fatty acid composition of
Bacteria (domain) varies from
species to species in where
chain length
and in the presence or absence
of double bonds, rings, branched
chains, or hydroxy groups
103
In FAME analyses, fatty acids extracted from cells
grown in culture under standardized conditions are
analyzed by what
gas chromatography
104
shows the types and amounts of fatty acids from the unknown bacterium
chromatogram
105
where is chromatogram results (types and amounts of fatty acids from the unknown bacterium) compared to?
database containing the fatty acid profiles of thousands of reference bacteria grown under the same conditions
106
FAME procedure
bacterial culture -> extract fatty acids -> derivatize to form methyl esters -> gas chromatography -> analyze the pattern of peaks from various fatty acid methyl esters -> compare pattern of peaks with patterns in database -> identify organism
107
can vary as a function of
temperature, growth phase (exponential versus
stationary), and growth medium
Fatty acid profiles of an organism
108
what is necessary for comparative results to be valid
grow the unknown organism on a specific medium
and at a specific temperature
109
generally highly dependent on
growth conditions,
Phenotypic characteristics of strains
110
may not well represent phenotypes present in the natural
environment
phenotypes observed in the laboratory
environment
111
can vary with the taxonomic
groups being examined
the value of different phenotypic characteristics for
reaching a firm systematics conclusion
112
how microbes are named and classifie
science of taxonomy
113
information in science of taxonomy are presented on
culture collections
114
what is culture collections
- repositories for scientific deposition of live microbial cultures
-key taxonomic resources available for microbiology; and on the
- procedures for naming new microbial species.
115
form an important foundation of the
systematics of prokaryotic species
formal description of a new microbial species and the deposition of
cultures into a culture collection
115
is the organization of organisms into progressively more
inclusive groups on the basis of either phenotypic similarity or
evolutionary relationship.
classification
116
A species is made up of what
one to several strains
117
grouped into genera (singular, genus)
similar species
118
Similar genera are grouped into
families, families into orders, orders into classes, up to the domain
119
the
highest-level taxon based on a collection of phenotypic and genotypic
information
domain
120
is the actual naming of organisms and follows the binomial
system of nomenclature
nomenclature
121
nomenclatures follows what
binomial system of nomenclature
122
binomial
system of nomenclature devised by who
Swedish medical doctor and
botanist Carl Linnaeus
123
what is given to organism through nomenclature
genus names and species epithets.
124
The creation of new taxa of Bacteria and Archaea must follow the rules
described in the
International Code of Nomenclature of Bacteria (the
Bacteriological Code)
125
what does the International Code of Nomenclature of Bacteria (the
Bacteriological Code) presents
formal framework by
which Bacteria and Archaea are to be officially named and the
procedures by which existing names can be changed
126
To achieve formal validation of taxonomic standing as a new genus
or species
a detailed description of the organism’s characteristics and
distinguishing traits, along with its proposed name, must be published,
and viable cultures of the organism must be deposited in at least two
international culture collections
127
A major vehicle for the description of new taxa
is
International Journal of Systematic and Evolutionary Microbiology
(IJSEM)
128
what is International Journal of Systematic and Evolutionary Microbiology
(IJSEM)
official publication of record for the taxonomy and
classification of Bacteria, Archaea, and microbial eukaryotes.
129
Two websites provide listings of valid, approved bacterial names
1. List of Prokaryotic Names with Standing in Nomenclature
2. Prokaryotic Nomenclature Up-to-Date
130
possible to use to
characterize the phenotypic and genotypic characteristics of
microorganisms without the need for the cultivation of an
isolated strain.
molecular and genomic techniques
131
with its absence, it is not
possible to validly name a new species of microorganism under
the Bacteriological Code
absence of an isolate that can be
deposited in two international culture collections
132
can be applied when an organism is well characterized but not yet cultured or not yet obtained in pure culture
a provisional taxonomic name
133
can be applied when an organism is well characterized but not yet cultured or
not yet obtained in pure culture,
provisional taxonomic name
134
appended to
candidate taxonomic ranks
moniker Candidatus
135
a globally widespread and well
characterized marine bacterium that is difficult to grow in
laboratory media, and so has not been formally named under
the Bacteriological Code.
“Candidatus
Pelagibacter ubique”
136
can be grown
in laboratory culture but the culture is not pure so this bacterium also
retains Candidatus status
“Candidatus Heliomonas lunata”
137
oversees the nomenclature and taxonomy of Bacteria and Archaea.
International Committee on the Systematics of Prokaryotes (ICSP)
138
The
ICSP also oversees the publication of
IJSEM and the International Code of
Nomenclature of Bacteria
139
ICSP gives guidance to
several subcommittees
that meet to establish and revise standards for the description of new
species in the different groups of Bacteria and Archaea.
140
classification system most widely accepted by
microbiologists
Bergey’s Manual of Systematic
Bacteriology
141
what is Bergey’s Manual of Systematic
Bacteriology
a major taxonomic treatment of Bacteria and
Archaea
142
Bergey’s Manual has served
microbiologists since
1923
143
Bergey’s Manual has served
microbiologists as
a compendium of information on
all recognized prokaryotic species
144
second major source describing the physiology, ecology, phylogeny,
enrichment, isolation, and cultivation of Bacteria and Archaea
The
Prokaryotes
145
The Prokaryotes describes unsa
physiology, ecology, phylogeny,
enrichment, isolation, and cultivation of Bacteria and Archaea
146
offer microbiologists
both the concepts and the details of the biology of Bacteria and Archaea
as we know them today and are the primary resources for microbiologists
characterizing newly isolated organisms
Bergey’s Manual and The Prokaryotes
147
important foundation of microbial systematics
National microbial culture collections
148
play an important role in protecting microbial biodiversity, just
as museums do in preserving plant and animal specimens for future study
culture collections
149
, microbial culture collections store
microorganisms as
viable cultures,
150
microbial culture collections are typically
frozen or in a freeze-dried
state to maintain the cells indefinitely in a living
state and prevent genetic changes that might occur if the organisms were
continually subcultured
151
A related and key role of culture collections is as repositories for
type strains
152
when is a strain designated as the type strain
When a new species of bacteria is described in a scientific
journal
153
type strain serves
as
nomenclatural type of the taxon for future taxonomic
comparison with other strains of that species
154
