Transcript Evolution, classification, and identification of bacteria

Evolution, classification, and
identification of bacteria
Early life on Earth
Naming microorganisms
Classifying and identifying microorganisms
Major groups of bacteria
Early life on Earth
0
Age of dinosaurs
1
Origin of metazoans
Origin of modern eukaryotes
Time before
present
(billions of
years)
2
Origin of oxygenic phototrophs
(cyanobacteria)
3
Origin of Life
4
__________ ___________
Formation of the earth
Early life on Earth
0
Age of dinosaurs
Origin of metazoans
20%
1
10%
Origin of modern eukaryotes
Time before
present
(billions of
years)
1%
2
Origin of oxygenic phototrophs
(cyanobacteria)
3
Origin of Life
4
Formation of the earth
0.1%
O2
(% in
atmosphere)
Anoxic
______________
Planktothrix
Lyngbya
http://www-cyanosite.bio.purdue.edu/
Early life on Earth
0
Age of dinosaurs
Origin of metazoans
20%
1
10%
Origin of modern eukaryotes
Time before
present
(billions of
years)
2
Endosymbiosis
Origin of oxygenic phototrophs
(cyanobacteria)
1%
0.1%
O2 (% in
atmosphere)
3
Origin of Life
4
Formation of the earth
Anoxic
Endosymbiosis -- the theory
that __________________
and __________________
are the descendants of
ancient prokaryotes from
the Domain “Bacteria”
An example of a new, developing endosymbiosis?
Legionella
bacteria
Newsome et al.
Appl Environ
Microbiol, May
1998, p. 16881693, Vol. 64,
No. 5
Giemsa stain showing the occurrence of bacteria in vacuoles of an amoeba
after 24 and 48 h of incubation at 25°C. Characteristic morphological
features of the amoeba host cell, such as the nucleus (arrowhead), were
intact. Bar, 20 µm.
The Endosymbiotic Theory
Developed mainly by Lynn Margulis (1970s)
Strong evidence supports the endosymbiotic origin of mitochondria and
chloroplasts



_________ similar to bacteria
Both have their own _______________, which are similar to those of bacteria
(“70S” prokaryotic-type)
mitochondria have their own__________, which is similar to that of bacteria
The latest hypothesis: ______________ themselves may have once been
endosymbiotic bacteria


Recently reported (Nature, 7/26/01) that bacteria live inside other bacteria in the
mealybug (not yet known what they are doing or what one does for the other).
Margulis theorizes that the nucleus arose when one type of bacterium moved
inside another.
Naming microorganisms
Binomial nomenclature
Homo sapiens
Escherichia coli
Pseudomonas aeruginosa
Text, Fig. 1.13
Classifying and identifying microorganisms
Taxonomy - study of the classification, organization, and
naming of living things.
One’s goal may be simply to organize and group by
_____________________ with no concern for natural
evolutionary relationships. Often referred to (confusingly) as
simply “taxonomy”.
Alternatively, one’s goal may be to reconstruct natural,
________________ relationships between organisms. Known
as “phylogeny”.
Classification can be based on phenotypic
or genotypic characteristics or both
• phenotype -- observable
_____________________ of an organism:
shape, size, metabolism, etc.
• genotype -- the precise ________________
constitution of an organism
Classification based on phenotype
Classification based on phenotype
Examples of phenotypic characteristics used to
differentiate prokaryotes:
Gram reaction, fermentation of sugar, cell morphology,
growth on a specific compound, etc.
These characteristics tell us little or nothing about the true
evolutionary relationships between organisms. They are
used simply (and very usefully) as a method for
___________________ them.
Identification methods are usually based on such
characteristics
Example of methods to be used for identification of a
newly isolated enteric bacterium
Isolation
of bacterium
from intestine of
warm-blooded animal
Obtain pure culture
Gram Reaction
Gram negative
rod-shaped
facultative
aerobe
ferments lactose, producing
acids and gas
Gram positive
not rod-shaped
obligately anaerobic
does not ferment lactose
confirmatory tests: (positive: indole, methyl red, etc.
(negative: citrate, Voges-Proskaur, H2S
Escherichia coli
Phylogenetics
Phylogeny -- The ordering of species into higher
___________ (classification categories) and the
construction of evolutionary trees, all based on
evolutionary (natural) relationships.
http://heg-school.awl.com/bc/companion/cmr2e/activity/AL/AL09b.htm
Phylogenetics
How similar are two organisms at the
level of the DNA?
2 primary methods for determining this. In both, the
same DNA___________________ from two
organisms is compared:
 DNA hybridization
i.e. Put strand from one organism together with strand
from another. How well do they ________________
to each other?
 DNA sequencing
X
X
X
X
X X
X
X
X
X
Calculating the
evolutionary
distance between
DNA molecules
Constructing a phylogenetic tree
from evolutionary distances
The 16S rRNA gene: a most useful molecule
for determining evolutionary relationships
Advantages
•
Every organism has it (eukaryotes have 18S
rRNA, which is related)
•
It’s “highly conserved” (i.e. it doesn’t
________________ quickly)
•
There are, however, regions which evolve more
_________________ than others
•
It doesn’t get transferred horizontally (or at least
transfer is very rare)
Overall, not only is the primary sequence of 16S rRNA molecules
highly conserved, but the secondary structure is, as well
But there are differences, and these differences represent
phylogenetic and phenotypic differences in the organisms
themselves
Anabaena cylindrica (Cyanobacteria)
Arthrobacter globiformis (Gram-positive)
Rhodococcus rhodochrous (Gram-pos itive)
Desulfovibrio des ulfuricans (Ž-Proteobacteria)
Rhodospirillum rubrum (
-Proteobact.)
Sphingomonas paucimobilis (
-Proteobact.)
Agrobacterium tumefaciens (
-Proteobact.)
-Proteobact.)
Rhodoplanes roseus (
GJ10
Aquabacter spiritensis (
Azorhizobium caulinodans (
-Proteobact.)
-Proteobact.)
Ancylobacter aquaticus (
WDD1
-Proteobact.)
Thiobacillus novellus (
-Proteobact.)
Burkholderia cepacia (
-Proteobact.)
-Proteobact.)
Es cherichia coli K12 (
Acinetobacter calcoaceticus (
Pseudomonas putida (
-Proteobact.)
-Proteobact.)
Pseudomonas stutzeri (
-Proteobact.)
"Flavobacterium" lutes cens (
-Proteobact.)
Pseudomonas balearicus (
WDHI
Ps.stutzeri ( -Proteobact.)
0.1
Evolutionary
relationships of
representative
bacteria based
on the
sequences of
their 16S rRNA
genes
-Proteobact.)
Boletus satanas str. TDB-1000 (mushroom) [100]
Scypha ciliata (sponge) [120]
Tripedalia cystophora (jellyfish) [124]
Styela plicata (sea squirt) [158]
Alligator mississippiensis [143]
Gallus gallus (chicken) [145]
Evolutionary
relationships of
representative
Eukaryotes based
on the sequences of
their 16S rRNA
genes
Mus musculus (common or house mouse) [150]
Homo sapiens (human) [149]
Rhinobatos lentiginosus (lesser sand shark) [135]
Bufo valliceps (African toad) [142]
Drosophila melanogaster (fruit fly) [161]
Crassostrea virginica (oyster) [176]
Gyliauchen sp. (flatworm) [192]
Glycine max var. Wayne (soybean) [261]
Paramecium tetraurelia (ciliate) [321]
0.1
Boletus satanas str. TDB-1000 (mushroom) [100]
Anabaena cylindrica (Cyanobacteria)
Arthrobacter globiformis (Gram-positive)
Scypha ciliata (sponge) [120]
Rhodococcus rhodochrous (Gram-positive)
Desulfovibrio desulfuricans (Ž-Proteobacteria)
Tripedalia cystophora (jellyfish) [124]
Rhodospirillum rubrum ( -Proteobact.)
Styela plicata (sea squirt) [158]
Sphingomonas paucimobilis ( -Proteobact.)
Agrobacterium tumefaciens ( -Proteobact.)
Alligator mississippiensis [143]
Rhodoplanes roseus ( -Proteobact.)
Gallus gallus (chicken) [145]
GJ10GJ10
Aquabacter spiritensis ( -Proteobact.)
Mus musculus (common or house mouse) [150]
Azorhizobium caulinodans ( -Proteobact.)
Ancylobacter aquaticus ( -Proteobact.)
WDD1
Homo sapiens (human) [149]
Rhinobatos lentiginosus (lesser sand shark) [135]
Thiobacillus novellus ( -Proteobact.)
Burkholderia cepacia ( -Proteobact.)
Bufo valliceps (African toad) [142]
Escherichia coli K12 ( -Proteobact.)
Drosophila melanogaster (fruit fly) [161]
Acinetobacter calcoaceticus ( -Proteobact.)
Pseudomonas putida ( -Proteobact.)
Crassostrea virginica (oyster) [176]
Pseudomonas stutzeri ( -Proteobact.)
"Flavobacterium" lutescens ( -Proteobact.)
Gyliauchen sp. (flatworm) [192]
Pseudomonas balearicus ( -Proteobact.)
WDHI
WDH1
Glycine max var. Wayne (soybean) [261]
Ps.stutzeri ( -Proteobact.)
0.1
Paramecium tetraurelia (ciliate) [321]
0.1
Early life on Earth
0
Age of dinosaurs
20%
Origin of metazoans
1
10%
Origin of modern eukaryotes
Endosymbiosis
Time before
present
(billions of
years)
1%
2
0.1%
Origin of oxygenic phototrophs
(cyanobacteria)
Bacteria
3
Archaea
?
Origin of Life
4
Chemical evolution
Formation of the earth
O2 (% in
atmosphere)
Nuclear line
(Eucarya)
Anoxic
Three Domains of Life
BACTERIA
ARCHAEA
EUCARYA
The Archaea
January 24, 2001
New Group of Microorganisms Discovered in the Open Sea
Archaea, one of three separate domains of life on our planet, were undiscovered until 1970.
Since then, they had been found mostly in extreme environments such as hightemperature volcanic vents on the ocean floor, continental hot springs and fumeroles,
and highly salty or acidic waters. Now, scientists funded by the National Science
Foundation (NSF) have found unexpected, astounding numbers of archaea living in
Earth's largest biome, the open sea.
The researchers--David Karl and Markus Karner of the University of Hawaii, and Edward
DeLong of the Monterey Bay Aquarium Research Institute--have published a paper in
this week's issue of the journal Nature on their discovery: "Archaeal dominance in the
mesopelagic zone of the Pacific Ocean." The concentration of archaea in their study
leads the scientists to conclude that archaea are "a large percentage of the biomass of
the open ocean," says Karl. "These organisms could make up 50 percent of life in the
open sea." The research is the first to note their numerical abundance.
Major groups (kingdoms) of the (true) Bacteria