Microbial Taxonomy and Systematics Flashcards
involves not just naming organisms but grouping them with other organisms that share common properties
Taxonomy
is involved in the classification and naming of organisms
taxonomy
is involved in the determination of evolutionary relationships of organisms.
systematics
ascertain the sharing of the common ancestry by different organisms
systematics
different organisms are scientifically named and grouped in different taxonomic levels
taxonomy or systematics?
taxonomy
organisms are grouped based on their evolutionary relationships.
systematics or taxonomy
systematics
can be considered as a branch of systematics
taxonomy
assigns every organism a kingdom, phylum, class, order, family, genus, and species, which, among other possibilities,
Linnean system of classification
mnemonic of Linnean system of classification
Kingdom
Phylum
Class
Order
Family
Genus
Species
. It was in 1735 when the two-kingdom system, Plantae and Animalia was formally introduced by Swedish botanist
Carolus Linnaeus
proposed to include bacteria and fungi in the plant kingdom
Carl von Nägeli
proposed the Kingdom Protista, to include bacteria, protozoa, algae, and fungi.
Ernst Haeckel
. The term prokaryote was then introduced in 1937 by
Edouard Chatton
what term is introduced to distinguish cells having no nucleus from the nucleated cells of plants and animals
prokaryote
cells in which the nuclear material (nucleoplasm) is not surrounded by a nuclear membrane
who defined prokarytoes this way
Roger Stanier
proposed the Kingdom Prokaryotae
Robert G.E. Murray
founded the five-kingdom system in which prokaryotes were placed in the Kingdom Prokaryotae, or Monera, and eukaryotes comprised the other four kingdoms.
Robert H. Whittaker
names only clades — groups of organisms that descended from a common ancestor.
phylogenetic classification system
DNA sequence-based phylogenetic analysis has revealed that the five kingdoms do not represent five primary evolutionary lines. Instead, cellular life on Earth has evolved along three primary lineages called
domains
contains the eukaryotes including the plants, animals, fungi, and protists.
what domain
Eukarya
Molecular studies in the 1970s revealed that the Archaea differed from all other bacteria in their what sequence and what structures
16s rRNA sequence
cell wall
membrane lipids
aspects of protein snythesis
are excellent tools for discerning evolutionary relationships because all cells contain ribosomes
rRNA (ribosomal RNAs)
an American microbiologist, pioneered the use of comparative rRNA sequence analysis as a measure of microbial phylogeny and, in so doing, revolutionized our understanding of cellular evolution.
Carl Woese
the greater the sequence variation between any two organisms, the greater/lesser their evolutionary divergence.
greater
The phylogenetic tree of life reveals two very important evolutionary facts:
(1) all prokaryotes are not phylogenetically closely related
(2) Archaea are actually more closely related to Eukarya than to Bacteria
The universal tree of life shows that LUCA resides very early within the ___ domain
Bacteria
largest group of bacteria
Proteobacteria
the most phylogenetically ancient phylum contains the genus
Aquifex
which are hyperthermophilic H2 (Hydrogen) – oxidizing chemolitotrop
Aquifex
green non-sulfur bacteria
Chloroflexus
follows Aquifex as the most phylogenetically acient phylum (3)
Thermodesulfobacterium
Thermotoga
Chloroflexus
the phototrophic green sulfur bacteria
Spirochetes
chemoorganotrophic bacteria (2)
Flavobacterium
Cytophaga
budding bacteria
Plantomyces
Verrucomicrobium group
Chlamydia
gram positive bacteria (2)
actinobacteria
firmicutes
mollicutes
along with his colleagues, constructed the phylogenetic trees for the prokaryotes, which showed evolutionary relatedness
Carl Woese
which differ from bacteria by its cell wall and plasma membrane chemistry, as well as the sequences of its 16S rRNA
Archaea
does Archaea and Bacteria have the same genetic material?
Yes
which domains have histones
Archaea
Eukarya
gene strucuture for three domains of life
introns absent/present
A = absent
B = absent
E = present
plasmids for three domains of life
common/rare
A = common
B = common
E = rare
polycistronic mRNA presence in three domains of life
present/absent
A = present
B = present
E = absent
ribosomes in three domains of life
70s/80s
A = 70s
B = 70s
E = 80s
which three domains of life are sensitive to streptomycin, chloramphenicol
Bacteria
initiator tRNA for each domain of life
A = Methionine
B = N-formyl methionine
C = Methionine
membrane fatty acids in three domains of life
ether linked, branched/ ester-linked, straight
A = ether-linked, branched
B = ester-linked, straight
E = ester-linked, straight
internal organelles presence in three domains of life
A = absent
B = absent
E = present
site of energy generation in three domains of life
A = cytoplasmic membrane
B = cytoplasmic membrane
E = mitochondira
presence of muramic in the cell wall in three domains of life
A = muramic acid absent
B = muramic acid present
E = muramic acid absent
have flattened square or triangular cells in domain Archaea
Haloarcula
which is composed of different substituted L-amino acids and polysaccharides
pseudomurein
have cell walls composed of a layer of proteinaceous subunits known as an ___, which is directly associated with the cell membrane
S-layer
This difference actually makes the Archaean members not susceptible to antibiotics such as penicillin and lysozyme, whose antibacterial action is specifically directed to peptidoglycan.
S-layer in Archaea
membranes, in which the lipid component of the part contains branched isoprenes instead of fatty acids
what domains
Archaea
found in extreme environments
Archaea
can live well at over 100 C what kind of Archaea
thermophilic
forms of Archaea can thrive in very cold environments, like in the Antarctic
psychropilic
The reason that this lay undetected for so long is that these organisms cannot as yet be cultured in the laboratory, and their presence can only be inferred by the use of modern DNA-based analysis
Archaea
The oldest known fossils are the remains of ____ that lived more than 3.5 billion years ago.
prokarytoes
cells evolved more recently, about 2.5 billion years ago
Eukaryotic cells
according to this theory, eukaryotic cells evolved from prokaryotic cells living inside one another, as endosymbionts
endosymbiotic theory
The original nucleoplasmic cell was prokaryotic. However, infoldings in its plasma membrane may have surrounded the nuclear region to produce a true
nucleus
endosymbiotic prokaryotes give rise to what organelles
mitochondria
chloroplast
organism in which the eukaryotic host and bacterium require each other for survival
Cyanophora paradoxa
Phylogenetic trees of species in the domain Eukarya have been constructed from comparative sequence analysis of what rRNA gene
18s
appears to give a skewed view of eukaryotic microbial evolution, it still clearly sorts the eukaryotes out as a distinct domain of life with evolutionary roots more closely tied to the Archaea than to the Bacteria.
18s rRNA sequencing
is the actual naming of organisms and follows the binomial system of nomenclature
Nomenclature
Nomenclature is the actual naming of organisms and follows the binomial system of nomenclature devised by the Swedish medical doctor and botanist
Carl Linnaeus
The creation of new names of Bacteria must follow the rules described in
The International Code of Nomenclature of Bacteria
Because taxonomy is largely a matter of scientific judgment, there is no “official” classification of Bacteria and Archaea. Presently, the classification system most widely accepted by microbiologists is that of
Bergey’s Manual of Systematic Bacteriology
, a reference that provides detailed information on the enrichment, isolation, and culture of Bacteria and Archaea
The Prokaryotes
. A major vehicle for the description of new taxa is the
International Journal of Systematic and Evolutionary Microbiology (IJSEM)
the official publication of record for the taxonomy and classification of Bacteria and Archaea.
IJSEM
is the study of the diversity of organisms and their relationships
systematics
traditionally has focused on practical aspects of identification and description, activities that have relied heavily on phenotypic comparisons
bacterial taxonomy
This polyphasic approach to taxonomy uses three kinds of methods (3)
phenotypic
genotypic
phylogenetic
analysis examines the morphological, metabolic, physiological, and chemical characteristics of the cell
what analysis
phenotypic
analysis considers characteristics of the genome
what analysis
Genotypic
Colony morphology; Gram reaction; cell size and shape; pattern of flagellation; presence of spores, inclusion bodies (e.g., PHB,a glycogen, or polyphosphate granules, gas vesicles, magnetosomes); capsules, S-layers or slime layers; stalks or appendages; fruiting-body formation
what category
morphology
Motility Nonmotile; gliding motility; swimming (flagellar) motility; swarming; motile by gas vesicles
what category
motility
Mechanism of energy conservation (phototroph, chemoorganotroph, chemolithotroph); utilization of individual carbon, nitrogen, or sulfur compounds; fermentation of sugars; nitrogen fixation; growth factor requirements
what category
metabolism
Physiology Temperature, pH, and salt ranges for growth; response to oxygen (aerobic, facultative, anaerobic); presence of catalase or oxidase; production of extracellular enzymes
what category
physiology
Cell lipid chemistry Fatty acids; polar lipids; respiratory quinones
what category
cell lipid chemistry
Cell wall chemistry Presence or absence of peptidoglycan; amino acid composition of cross-links; presence or absence of cross-link interbridge
what category
cell wall chemistry
other traits for phenotypic characteristics
Cell wall chemistry Presence or absence of peptidoglycan; amino acid composition of cross-links; presence or absence of cross-link interbridge
genotypic method that Genome-wide comparison of sequence similarity. Useful for distinguishing species within a genus
DNA-DNA hybridization
Ribotyping (Section 16.9), AFLP, rep-PCR (Figure 16.21). Rapid method to distinguish between species and strains within a species
genotypic method
DNA profiling
strain typing using DNA sequences of multiple genes (Figure 16.22). High resolution, useful for distinguishing even very closely related strains within a species
what genotypic methods
Multilocus sequence typing
Percentage of guanine–cytosine base pairs in the genome. If the GC ratio of two organisms differs by more than about 5%, they cannot be closely related, but organisms with similar or even identical GC ratios may be unrelated. Not much used now in taxonomy because of poor resolution
what genotypic method
GC ratio
The evolutionary history of a group of organisms is called its
phylogeny
___ is inferred indirectly from nucleotide sequence data. Our premises are that (1) all organisms are related by descent, and (2) that the sequence of DNA in a cell’s genome is a record of the organism’s ancestry.
phylogeny
is a process of inherited nucleotide sequence change, comparative analyses of DNA sequences allow us to reconstruct phylogenetic histories
evolution
The most widely used and useful for defining relationships in prokaryotes is the gene encoding
16s rRNA (prokaryotes)
18s rRNA (eukaryotes)
sequences of shared evolutionary ancestry that encode functionally equivalent molecules.
homologous sequences
If sequences do change at a constant rate, such pairs would serve as an approximate
molecular clock
relies heavily on the polymerase chain reaction (PCR) to obtain sufficient copies of a gene for reliable sequencing
DNA sequence
analysis of DNA sequences that are related by common ancestry
homology
Once the DNA sequence of a gene is obtained, the next step in phylogenetic analysis is to align that sequence with homologous sequences from other organisms. By doing this, nucleotide mismatches and insertions and deletions, some of which may be phylogenetically informative, can be pinpointed.
what analysis
sequence alignment
which is a graphic depiction of the relationships among sequences of the organisms under study, much like a family tree.
phylogenetic tree
branches represent species that exist now and from which the sequence data were obtained.
what part of phylogenetic tree
tips
are points in evolution where an ancestor diverged into two new organisms, each of which then began to evolve along its separate pathway.
what part of phylogenetic tree
nodes
define both the order of descent and the ancestry of the nodes,
what part of phylogenetic tree
branches
represents the number of changes that have occurred along that branch.
branch length
combines phenotypic, genotypic, and sequence-based phylogenetic data within a framework of standards and guidelines for describing and identifying prokaryotes, but the issue of what actually constitutes a prokaryotic species remains controversial
microbial systematics
is defined operationally as a group of strains sharing a high degree of similarity in several independent traits.
prokaryotic species
Traits currently considered most important for grouping strains together as a species include ___% or greater genomic DNA–DNA hybridization
70 percent
percent or grater identity in 16s rRNA sequence to group strains together as a species
98%
How do new prokaryotic species arise? A likely possibility is by the process of
periodic purges and selection
If cells in this population share a particular resource (for example, a key nutrient), the population is considered an
ecotype
Biological systematics encompasses three distinct activities:
taxonomy
classification
nomeclature
commonly used outside the biological
systematic community as almost any animate or inanimate object, place, concept or event can be
classified according to some criteria or scheme.
classification
e act of assigning individuals to a class or
classes based on some common relations or affinities.
classification
classifications may be represented by assignment of ‘taxonomic’ rank (species, genera, families,
superfamilies, orders etc.) or by evolutionary scenarios.
what systematics
evolutionary systematics
interacts with both taxonomy and nomenclature
classification
view natural groups as those taxa linked by the greatest similarity to one another
phenetists
s consider natural groups to be monophyletic, and natural classifications to reflect
organismal history.
cladist
e is defined as referring to
the most recent Common ancestor of two designated taxa and its descendants
node
defined as referring to all organisms sharing a more recent common
ancestor with one designated taxon than with a second such taxon (
stem
defined as referring to the first ancestor to evolve a designated character (bar) and its
descendants (
apomorphy
Science of classification,
Objective: classify, establish
relationship and differences
The theory and practice…
Reference for newer microorganisms
A universal language for scientist
Taxonomy
determination of the evolutionary
relationship/common ancestry
consists of both taxonomy and evolution.
Involves cladistics, and phylogenetics.
Systematics
refers to the classification of
organisms based on the branching of
different lineages from a common
ancestor.
Cladistics
refers to the study of the
history of evolution and the relationship
among groups of organisms.
Phylogenetics
§ assigns every organism a kingdom, phylum, class, order,
family, genus, and species, which, among other possibilities,
has the handy
Linnean System
§ Two-kingdom System
Linnean System
created long before scientists understood that organisms
evolved.
§ not based on evolution; most biologists are switching to a
classification system that reflects the organisms’ evolutionary
history.
Linnean system
inclusion of bacteria and
fungi in plant kingdom
who included
Carl von Nageli
who defined - definition
of prokaryote
Edouard Chatton
Roger Stanier
proposed the Kingdom
Prokaryotae.
Robert G.E Murray
addition of
Kingdom Protista to
include bacteria, protozoa,
algae, and fungi
who
Ernst Haeckel
§ A phylogenetic tree based on 16s rRNA gene data, showing the
separation of bacteria, archaea, and eukaryotes by
Carl Woese
also differ in their cell wall structure, membrane lipids and
aspects of protein synthesis from bacteria.
Archaea
major taxonomic treatment
of Bacteria and Archaea.
Bergey’s Manual of Systematic Bacteriology
- a
reference that provides
detailed information on the
enrichment, isolation, and
culture of Bacteria and
Archaea
The Prokaryotes
gramnegative cell walls, thinskinned i.e E. coli
Proteobacteria
– gram-positive
cell walls, thick skinned i.e.
bacilli
Firmicutes
– lack a cell
wall & are soft i.e
Mycoplasma
Tenericutes
– i.e
actinomycetes
Actinobacteria
group of microorganisms (5)
bacteria (archeans, eubacteria)
protists (algae, protozans, slime molds)
fungi (yeast and molds)
helminths
viruses, viroids, prions (acellular)
not classified as part of
any of the three domains.
virus
population of
viruses with similar characteristics
(including morphology, genes, and
enzymes) that occupies a particular
ecological niche ~ International
Committee on Taxonomy of Viruses
viral species
Closely related organisms that can interbreed
eukaryotic species
population of cells with similar characteristics.
prokaryotic species
– pure cultures of one species which are
not 100% identical
strain
Traits currently considered most important for
grouping strains together as a species
* __% or greater genomic DNA–DNA
hybridization
70
Traits currently considered most important for
grouping strains together as a species
___% or greater identity (3% difference) in
16S rRNA gene sequence
97
Which among can be used to classify/identify microorganisms? (Select all that applies)
using 16s rRNA
DNA fingerprinting
interbreeding behaviors
ecological characteristics
morphologic characteristics
morphologic characteristics
using 16S rRNA
DNA fingerprinting
During the second golden age of microbiology, __ was established as the __ material
DNA
genetic
Which field of microbiology studies bacterial taxonomy and systematics
Evolutionary microbiology
cell membrane with lipid monolayer
Archaea
includes the mitochondria and chloroplast
bacteria
with multiple linear chromosomes
eukarya
Koch established the postulate for the __ theory
germ
Whose discovery paved the way to unraveling the microscopic world of bacteria?
Leeuwenhoek
Microbiology became established during the times when spontaneous generation theory was being promoted.
T/F
False
Who among the following disproved the theory of abiogenesis? (Select all that applies)
Pasteur
Spallanzani
Rediehrlich
needham
Leeuwenhoek
Pasteur
Spallanzani
Redi
first man (Y chromosome) is what race
African
LUCA means
Last Universal Common Ancestor
similar to bacteria (compared to eukarya)
mitochondrial gene
one gene > one mRNA > 1 protein (___)
one gene > one mRNA > 3 protein (___)
traditionally
polycystronic
plasmids is only present in what eukaryotic organism
yeast
ribosomes in eukarya
80s
70s (mitochondrion)
(additional properties, characteristics of a species
strain
smell during the rainy season
- look like fungi when grown in culture bacteria
actinobacteria
are not included in the domain because they do not have ribosomes
viruses
species can be determined based on
___
reproducibility
n cooked rice, spores germinate causing sliminess or ice
bacillus cereus
causes anthrax
Bacillus anthracis
