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MicrobiologyBrock 13th edition: chapters 1, 16
a. Evolution of life
b. Microbial evolution
c. Examples for universal importance of bacteria in biology, environment and health
Why study Microbiology ?
Figure 1.6a
Mammals Humans
Vascularplants
Shellyinvertebrates
Algaldiversity
Origin ofcellular life
Moderneukaryotes
Origin ofcyanobacteria
20% O2
O2
AnoxicEarth
Earthis slowlyoxygenated
Present
Mic
rob ial life for ms only
Origin of Earth(4.6 bya)
1bya
2bya
3bya
4bya
Anoxygenicphototrophicbacteria
a. Evolution of life
Figure 16.4
EarlyBacteria
EarlyArchaea
Mound:precipitates of clay,metal sulfides, silica,and carbonates
Ocean water(20°C, containingmetals, CO2 andPO4
2)
Flow of substancesup through mound
Ocean crust
Nutrients in hothydrothermal vent water
Aminoacids
Sugars
Nitrogenbases
Evolution of life
Figure 16.4
Evolution of life
Tim
e
(0.
3 to
0.5
bil
lio
n y
ears
)
1. Prebiotic chemistry
2. “RNA world”
3. proteolipid membrane
4. LUCA (last universal common ancestor)
5. diversification, interaction
6. Dispersal (other habitats)
Figure 16.7
In
OutPrimitivehydrogenase
PrimitiveATPase
Cytoplasmicmembrane
S0 reductase
LUCA’s energy metabolism
S + H2 H2S ΔG0’ = -20,6 kJ
e--acceptor e--donor
pyrite H+ gradient
LUCA’s C-metabolism
S + H2 H2S ΔG0’ = -20,6 kJ
CO2 fixation organic compounds (i.e. acetate)
Chemoorganotrophic bacteria“metabolic diversification”
accumulate
4-4.3 x109 years BC
Metabolic diversification
S + H2 H2S ΔG0’ = -20,6 kJ
CO2 fixation organic compounds
Bacteria
accumulate
4-4.3 x109 years BC
Archaea
3.7 x109 years BCH2, CO2 acetate 4 H2 + CO2 CH4 + 2H2O
methanogenesis
H3CCOO- + H2O CH4 + HCO3-
Bacteria: evolve phototrophy
S + H2 H2S ΔG0’ = -20,6 kJ
CO2 fixation organic compounds
Bacteria
accumulate
4-4.3 x109 years BC
Archaea
3.7 x109 years BCH2, CO2 acetate 4 H2 + CO2 CH4 + 2H2O
methanogenesis
H3CCOO- + H2O CH4 + HCO3-
3.3 x109 years BC Anaerobic phototrophy (H2S S)
2.7 x109 years BC Oxygen generating phototrophy (H2O O2)
CO2 fixation
CO2 fixation
Figure 16.6 and 8
Metabolichighlights
O2level
BYAEon Organisms,events
Phanaerozoic
Proterozoic
Archaean
Hadean
Cambrian
Precambrian
Anoxic
Extinction of the dinosaurs
Early animals
Multicellulareukaryotes
First eukaryoteswith organelles
Ozone shield
Great oxidation event
Cyanobacteria
Purple and green bacteria
Bacteria/Archaeadivergence
First cellular life; LUCA
Formation ofcrust and oceans
Formation of Earth4.5
4.0
3.5
3.0
2.5
2.0
1.5
1.0
0.5
0
20%
10%
1%
0.1%
Endosymbiosis?
Aerobic respiration
Oxygenic photosynthesis(2H2O O2 4H)
Sulfate reductionFe3 reduction
Anoxygenic photosynthesis
Acetogenesis
Methanogenesis
Sterile Earth
First: Fe-oxidation
Precambrian Fe3+ sediments
O2 toxicityNew metabolic pathways: - sulfate reduction - nitrification - chemolithotrophy - O2 respiration (grow fast)
Figure 16.9
Bacteria BacteriaEukarya EukaryaArchaea Archaea
cyanobacterium
Ancestor ofmitochondrion(Bacteria)
Animals Plants PlantsAnimals
Archaeonwith nucleus
nucleus formed
cyanobacterium
Engulfment of aH2-producing cellof Bacteria by aH2-consuming cellof Archaea
Endosymbiont theory of Eukaryote evolution
a) From nucleated Archaeon b) Hydrogen hypothesis
three take home messages
1. Bacteria are the ancient form of life. All other organisms evolved
from this. LUCA existed probably 4.3 Bio years ago.
2. All forms of life had extreme effects on their environment... and mediated dramatic change
3. Intense interactions. All organisms have interacted with each other
(directly or indirectly). E.g. Eukaryotes have always been interacting
intensely with bacteria throughout their evolution. The evolution and
function of one cannot be understood in the absence of the other.
b. Bacteria and Archaea evolution
Very high rate of evolution!!
1. Haploid genomes
2. Rapid growth
3. Large populations
Figure 16.10
Wild-type cellPigment mutantsLightDark
Mutantslost inlight
Mutantselectedin dark
Cell populations
Pigment mutants
Wildtype
Subculture number
Bac
teri
och
loro
ph
yll
a/m
l o
f cu
ltu
re 15
10
5
5 10 15 20
54321
Bacteria/ Archaea evolution
Rhodobacter capsulatus
16S rRNA
Phylogenetic analysis of Bacteria, Archaea
Ribosomal RNA genes
Va
ria
ble
……
.co
ns
erv
ed
Base position in 16S RNA gene
16S (bacteria), 18S (Eukaryotes)• Ubiquitous and essential• Ancient• Easy RNA isolation• Conserved and variable regions• Sufficiently long
Small ribosomal subunit RNA sequence: “long distance” relationships
Phylogenetic analysis of Bacteria, Archaea
conserved protein-coding genes: “long distance” and strain differentiation
EF-Tu (protein biosynth.)
Hsp60
aatRNA synthetases
…
Figure 16.12, 13
Kilo-bases 1 2 3 4 5
3.0–
2.0–
1.5–
1.0–
0.5–
16 S gene
Ancestralcell
Distinctspecies
Distinctspecies
Align sequences;generate tree
Sequence
Run on agarosegel; check forcorrect size
Amplify 16Sgene by PCR
Isolate DNA
A C G G T
Phylogenetic analysis
via 16S rDNA
Beforealignment
Afteralignment
Species 1
Species 1
Species 2
Species 2
Nonidentities
Gaps
9
15
Figure 16.14
Unrooted tree
Rooted trees
node
Relative relationships Defines unique paths of evolutionEmploys “outgroup”
Display phylogenetic relationshipCladistics = grouping by common features (absent in more distant relatives)Parsimony = assumes least number of steps
Figure 16.16
Bacteria Archaea Eukarya
PROKARYOTES EUKARYOTES
LUCA
Flavobacteria
Thermotoga
Thermodesulfobacterium
Aquifex
Cyanobacteria
Chloroplast
Proteobacteria
Mitochondrion
Gram-positivebacteria
Green nonsulfurbacteria
Crenarchaeota
Euryarchaeota
Thermoproteus
Pyrodictium
Thermococcus
MarineCrenarchaeota
Methano-bacterium
Methano-coccus
Pyrolobus
Methanosarcina
Thermoplasma
Methanopyrus
Extremehalophiles
Entamoebae Slimemolds
Animals (7.7 Mio species)
Fungi (0.6 Mio species)
Plants (0.3 Mio spec.)
Ciliates
Flagellates
Trichomonads
Microsporidia
Diplomonads(Giardia)
Universal phylogenetic tree
3 “domains”
Extensive geneticexchange??
> 80 phyla> 10 Mio species??
2 major phyla 8 Mio species ?
c. Current topics of interest
Methods: for analyzing microorganisms
Philosophy: the bacterial species problem
health: effects of the microbiota
environment: metabolic effects on C, N, P, S… cycles
Industry/safety: genetic engineering
health: what is a pathogen? How to kill bacteria?
Analyzing Bacteria and Archea
Physiology: << 5 % of all bacteria have been cultured
phenotype (motility, morphology, metabolism…)
FISH (Fluorecence in situ hybridization): DNA-oligo binding rRNA
Bacillus
Yeast
DNA sequencing (fast evolving field!!):
- 16S “community sequencing”
- “metagenome sequencing”
predict genes/metabolism
predict physiology
Universal probe eukaryal probe
Costs of DNA sequencing
Figure 22.16
Communitysampling approach
Environmentalgenomics approach
Outcomes
Single-gene phylogenetic tree Total gene pool of the community
1. Identification of all gene categories2. Discovery of new genes3. Linking of genes to phylotypes
Phylogenetic snapshotof most members of the community
1.
Identification of novelphylotypes
2.
Amplify single gene,for example, geneencoding 16S rRNA
Restriction digest total DNA andthen shotgun sequence, ORsequence directly (withoutcloning) using a “next generation”DNA sequencer
Extract totalcommunity DNA
Microbialcommunity
Sequence andgenerate tree Assembly and
annotation
DNA
Partialgenomes
DNA sequencing for microbial community analysis
Example 1: The gut microbiotaRole in health and diseases
Animal evolution
=>>
Animal evolution
A long history of co-evolution
Example 1: The gut microbiotaRole in health and diseases
Energy: acetate, butyrate
Vitamins: K, B12, C, niacin,panthotenic acid, biotin,folic acid
GALT: maturation
Colonization resistance
Innate defense: priming
Inflammatory bowel disease: stimulus
Mucosa: maturation
Th17 immune responses: stimulus
Host metabolism: stimulus
Microbiota enzyme/function MAMP signaling/innate immunity
Disease
Health
Example 1: The gut microbiotaRole in health and diseases
cancer: stimulus ?
Dethlefsen, 2008, Nature 448, pp. 811ff
Example 1: The gut microbiotaRole in health and diseases
Example 2: The “bacterial species problem”
Plants/animals: cross fertile offspring
Bacteria, Archaea: ??
Example 2: The “bacterial species problem”
The “bacterial species problem”
Phylogenetic tree181 genomes
proteobacteriales
Dagan et al., 2008, PNAS 105, pp. 10039 ff.
Phylogenomic tree≥5 genes exchanged by «horizontal gene transfer»
Streptococcus
Fraser et al., 2009, Science 323, pp. 741ff
The “bacterial species problem”
Bacteria, Archaea: - no sexual cycle - “long distance” gene exchange phylogenetic species concept niche occupation: “ecotype”
16S rRNA Gene Tree Multigene Tree
ATCC 11040T
ATCC 51760T
BAA-1194T
50 changes
Photobacterium damselae
Photobacterium leiognathi
Photobacterium mandapamensis
Photobacterium angustum
Photobacterium phosphoreum
Photobacterium iliopiscarium
Photobacterium kishitanii
Photobacteriumphosphoreum
Photobacteriumiliopiscarium
Photobacteriumkishitanii
FS-2.1FS-4.2FS-3.1FS-5.1FS-2.2
FS-5.2
ATCC 51761NCIMB 13476
NCIMB 13478NCIMB 13481
chubb.1.1ckamo.3.1canat.1.2
hstri.1.1calba.1.1
apros.2.1ckamo.1.1
vlong.3.1
The “bacterial species problem”
Figure 16.25
One microbial habitat
Ecotype I Ecotype II
Ecotype III
New speciesof Ecotype III
Cell containingan adaptivemutation
Populationof mutantEcotype III
Periodic selection
Adaptive mutantsurvives. OriginalEcotype III wild-typecells out competed
Repeat processmany times
The “bacterial species problem” ecotypes
Classification: traditional approach
Taxonomic systems:
Bergey’s Manual of Systematic Bacteriology
The Prokaryotes
International Committee on Systematics of Prokaryotes
Example 3: global Carbon-cycle
Humanactivities
Biological pump
Death andmineralization
Respiration
CO2
CO2
CO2
Landplants
Aquaticplants and
phyto-plankton
Animals andmicroorganisms
Fossilfuels
Humus
Soil formation
Earth’s crust Rock formation
Aquaticanimals
Figure 24.1
CH4
CH4, a greenhouse gas
CH4
Atmosphere 0.003
Example 3: global Carbon-cycle
Figure 24.2
Organic matter
Organic matter
Syntrophassisted
Oxygenic photosynthesis
Chemolithotrophy
Respiration
Methanotrophy
Methanogenesis
Acetogenesis
Anoxygenicphotosynthesis
OxicAnoxic
Anaerobicrespirationandfermentation
(CH2O)n
CO2
(CH2O)n
Example 3: anaerobic methane oxidation
Figure 14.28
Methanotrophic Archaea(ANME-types)Sulfate-reducing Bacteria
Organiccompounds
Marine sediments
c. Current topics of interest
Methods: for analyzing microorganisms
Philosophy: the bacterial species problem
health: effects of the microbiota
environment: metabolic effects on C, N, P, S… cycles
Industry/safety: genetic engineering
health: what is a pathogen? How to kill bacteria?