Transcript 14.1 Formation and Early History of Earth

Chapter 14
Microbial Evolution
and Systematics
I. Early Earth and the Origin and Diversification of Life
 14.1 Formation and Early History of Earth
 14.2 Origin of Cellular Life
 14.3 Microbial Diversification: Consequences for
Earth’s Biosphere
 14.4 Endosymbiotic Origin of Eukaryotes
14.1 Formation and Early History of Earth
 The Earth is ~ 4.5 billion years old
 First evidence for microbial life can be found in
rocks ~ 3.86 billion years old (southwestern Green
land)
Ancient Microbial Life
3.45 billion-year-old rocks, South Africa
Figure 14.1
14.1 Formation and Early History of Earth
 Stromatolites
 Fossilized microbial mats consisting of layers of filamentous
prokaryotes and trapped sediment
 Found in rocks 3.5 billion years old or younger
 Comparisons of ancient and modern stromatolites provide
evidence that
 Anoxygenic phototrophic filamentous bacteria formed ancient
stromatolites (relatives of the green nonsulfur bacterium
Chloroflexus)
 Oxygenic phototrophic cyanobacteria dominate modern
stromatolites
Ancient and Modern Stromatolites
3.5 billion yrs old
Oldest (Western Australia)
1.6 billion yrs old
(Northern Australia)
Modern stromatolites
(Western Australia)
Modern stromatolites
(Western Australia)
Modern stromatolites
(Yellow Stone NP)
Figure 14.2
More Recent Fossil Bacteria and Eukaryotes
From 1 billion yrs old
rocks in Central Australia
Prokaryotes (bacteria)
Eukaryotic cells
Figure 14.3
14.2 Origin of Cellular Life
 Early Earth was anoxic and much hotter than
present day (over 100 oC)
 First biochemical compounds were made by abiotic
systems that set the stage for the origin of life
 Surface origin hypothesis
 Contends that the first membrane-enclosed, selfreplicating cells arose out of primordial soup rich in
organic and inorganic compounds in ponds on Earth’s
surface
 Dramatic temperature fluctuations and mixing from
meteor impacts, dust clouds, and storms argue against
this hypothesis
 Subsurface origin hypothesis
 States that life originated at hydrothermal springs on
ocean floor
 Conditions would have been more stable
 Steady and abundant supply of energy (e.g., H2 and H2S)
may have been available at these sites
Submarine Mound Formed at Ocean Hydrothermal Spring
Cooler, more oxidized, more
acidic ocean water
Hot, reduced, alkaline
hydrothermal fluid
Figure 14.4
 Prebiotic chemistry of early Earth set stage for selfreplicating systems
 First self-replicating systems may have been RNAbased (RNA world theory)
 RNA can bind small molecules (e.g., ATP, other
nucleotides)
 RNA has catalytic activity; may have catalyzed its own
synthesis
A Model for the Origin of Cellular Life
Last Universal Common Ancestor
Figure 14.5
 DNA, a more stable molecule, eventually became
the genetic repository
 Three-part systems (DNA, RNA, and protein)
evolved and became universal among cells
 Other important steps in emergence of cellular life
 Build up of lipids
 Synthesis of phospholipid membrane vesicles that
enclosed the cell’s biochemical and replication
machinery
 May have been similar to vesicles synthesized on the
surfaces of montmorillonite clay
Lipid Vesicles Made in the Laboratory from Myristic Acid
vesicle
RNAs
Vesicle synthesis is catalyzed by the surfaces of montmorillonite
clay particles.
Figure 14.6
 Last universal common ancestor (LUCA)
 Population of early cells from which cellular life may
have diverged into ancestors of modern day Bacteria
and Archaea
 As early Earth was anoxic, energy-generating
metabolism of primitive cells was exclusively
 Anaerobic and likely chemolithotrophic
(autotrophic)
 Obtained carbon from CO2
 Obtained energy from H2; likely generated by H2S
reacting with FeS or UV light
Major Landmarks in Biological Evolution
Figure 14.7
A Possible Energy-Generating Scheme for Primitive Cells
Figure 14.8
 Early forms of chemolithotrophic metabolism would
have supported production of large amounts of organic
compounds
 Organic material provided abundant, diverse, and
continually renewed source of reduced organic carbon,
stimulating evolution of various chemoorganotrophic
metabolisms
14.3 Microbial Diversification
 Molecular evidence suggests ancestors of Bacteria
and Archaea diverged ~ 4 billion years ago
 As lineages diverged, distinct metabolisms developed
 Development of oxygenic photosynthesis dramatically
changed course of evolution
 ~ 2.7 billion years ago, cyanobacterial lineages developed
a photosystem that could use H2O instead of H2S,
generating O2
 By 2.4 billion years ago, O2 concentrations raised to 1 part
per million; initiation of the great oxidation event
 O2 could not accumulate until it reacted with abundant
reduced materials (i.e., FeS, FeS2) in the oceans
 Banded iron formations: iron oxides (e.g. Fe2O3) in
laminated sedimentary rocks; prominent feature in
geological record
Banded Iron Formations
Iron oxides
Figure 14.9
 Development of oxic atmosphere led to evolution of
new metabolic pathways that yielded more energy
than anaerobic metabolisms
 Oxygen also spurred evolution of organellecontaining eukaryotic microorganisms
 Oldest eukaryotic microfossils ~ 2 billion years old
 Fossils of multicellular and more complex eukaryotes
are found in rocks 1.9 to 1.4 billion years old
 Consequence of O2 for the evolution of life
 Formation of ozone layer that provides a barrier against
UV radiation
 Without this ozone shield, life would only have continued
beneath ocean surface and in protected terrestrial
environments
14.4 Endosymbiotic Origin of Eukaryotes
 Endosymbiosis
 Well-supported hypothesis for origin of eukaryotic cells
 Contends that mitochondria and chloroplasts arose
from symbiotic association of prokaryotes within
another type of cell
 Two hypotheses exist to explain the formation of
the eukaryotic cell
1) Eukaryotes began as nucleus-bearing lineage that
later acquired mitochondria and chloroplasts by
endosymbiosis
2) Eukaryotic cell arose from intracellular association
between O2-consuming bacterium (the symbiont), which
gave rise to mitochondria, and an archaean host
 Both hypotheses suggest eukaryotic cell is chimeric
 This is supported by several features
 Eukaryotes have similar lipids and energy metabolisms
to Bacteria
 Eukaryotes have transcription and translational
machinery most similar to Archaea
Major Features Grouping Bacteria or Archaea with Eukarya
Table 14.1
II. Microbial Evolution
 14.5 The Evolutionary Process
 14.6 Evolutionary Analysis: Theoretical Aspects
 14.7 Evolutionary Analysis: Analytical Methods
 14.8 Microbial Phylogeny
 14.9 Applications of SSU rRNA Phylogenetic Methods
14.5 The Evolutionary Process
 Mutations
 Changes in the nucleotide sequence of an organism’s
genome
 Occur because of errors in the fidelity of replication, UV
radiation, and other factors
 Adaptative mutations improve fitness of an organism,
increasing its survival
 Other genetic changes include gene duplication,
horizontal gene transfer, and gene loss
14.6 Evolutionary Analysis: Theoretical Aspects
 Phylogeny
 Evolutionary history of a group of organisms
 Inferred indirectly from nucleotide sequence data
 Molecular clocks (chronometers)
 Certain genes and proteins that are measures of
evolutionary change
 Major assumptions of this approach are that nucleotide
changes occur at a constant rate, are generally neutral, and
random
 The most widely used molecular clocks are small
subunit ribosomal RNA (SSU rRNA) genes
 Found in all domains of life
 16S rRNA in prokaryotes and 18S rRNA in eukaryotes
 Functionally constant
 Sufficiently conserved (change slowly)
 Sufficient length
Ribosomal RNA
16S rRNA
from E. coli
Figure 14.11
 Carl Woese
 Pioneered the use of SSU rRNA for phylogenetic
studies in 1970s
 Established the presence of three domains of life:
 Bacteria, Archaea, and Eukarya
 Provided a unified phylogenetic framework for bacteria
 The ribosomal database project (RDP)
 A large collection of rRNA sequences
 Currently contains > 409,000 sequences
 Provides a variety of analytical programs
14.7 Evolutionary Analysis: Analytical Methods
 Comparative rRNA sequencing is a routine
procedure that involves
 Amplification of the gene encoding SSU rRNA
 Sequencing of the amplified gene
 Analysis of sequence in reference to other sequences
PCR-Amplification of the 16S rRNA Gene
Figure 14.12
General PCR Protocol
 The first step in sequence analysis involves
aligning the sequence of interest with sequences
from homologous (orthologous) genes from other
strains or species
Alignment of DNA Sequences
Figure 14.13
 BLAST (basic local alignment search tool)
 Web-based tool of the National Institutes of Health
 Aligns query sequences with those in GenBank
database
 Helpful in identifying gene sequences
 Phylogenetic Tree
 Graphic illustration of the relationships among
sequences
 Composed of nodes and branches
 Branches define the order of descent and ancestry of
the nodes
 Branch length represents the number of changes that
have occurred along that branch
Phylogenetic Trees: Unrooted (a) and Rooted (b-d) Forms
Figure 14.14
 Evolutionary analysis uses character-state methods
(cladistics) for tree reconstruction
 The higher the proportion of characteristics that two organisms
share, the more recently they diverged from a common ancestor
 Cladistic methods
 Define phylogenetic relationships by examining changes in
nucleotides at individual positions in the sequence
 Use those characters that are phylogenetically informative
and define monophyletic groups (a group which contains all
the descendants of a common ancestor; a clade)
Identification of Phylogenetically Informative Sites
Dots: neutral sites.
Arrows: phylogenetically informative sites, varying in at least two of the sequences.
Figure 14.15
 Common cladistic methods
 Parsimony
 Maximum likelihood
 Bayesian analysis
14.8 Microbial Phylogeny
 The universal phylogenetic tree based on SSU rRNA
genes is a genealogy of all life on Earth
Universal Phylogenetic Tree as Determined by rRNA Genes
Figure 14.16
 Domain Bacteria
 Contains at least 80 major evolutionary groups (phyla)
 Many groups defined from environmental sequences
(metagenome)alone
 i.e., no cultured representatives
 Many groups are phenotypically diverse
 i.e., physiology and phylogeny not necessarily linked
 Eukaryotic organelles originated within Bacteria
 Mitochondria arose from Proteobacteria
 Chloroplasts arose from the cyanobacterial phylum
 Domain Archaea consists of two major groups
 Crenarchaeota
 Euryarchaeota
 Each of the three domains of life can be
characterized by various phenotypic properties
Major Features Distinguishing Prokaryotes from Eukarya
Major Features Distinguishing Prokaryotes from Eukarya
14.9 Applications of SSU rRNA Phylogenetic Methods
 Signature Sequences
 Short oligonucleotides unique to certain groups of organisms
 Often used to design specific nucleic acid probes
 Probes
 Can be general or specific
 Can be labeled with fluorescent tags and hybridized to rRNA
in ribosomes within cells
 FISH: fluorescent in situ hybridization
 Circumvent need to cultivate organism(s)
Fluorescently Labeled rRNA Probes: Phylogenetic Stains
Stained with universal
rRNA probe
Stained with a
eukaryotic rRNA probe
Figure 14.17
 PCR can be used to amplify SSU rRNA genes from
members of a microbial community
 Genes can be sorted out, sequenced, and analyzed
 Such approaches have revealed key features of
microbial community structure and microbial
interactions
 Ribotyping
 Method of identifying microbes from analysis of DNA
fragments generated from restriction enzyme digestion
of genes encoding SSU rRNA
 Highly specific and rapid
 Used in bacterial identification in clinical diagnostics
and microbial analyses of food, water, and beverage
Ribotyping
Figure 14.18
III. Microbial Systematics
 14.10 Phenotypic Analysis
 14.11 Genotypic Analysis
 14.12 Phylogenetic Analysis
 14.13 The Species Concept in Microbiology
 14.14 Classification and Nomenclature
14.10 Phenotypic Analysis
 Taxonomy
 The science of identification, classification, and
nomenclature
 Systematics
 The study of the diversity of organisms and their
relationships
 Links phylogeny with taxonomy
 Bacterial taxonomy incorporates multiple methods
for identification and description of new species
 The polyphasic approach to taxonomy uses three
methods
1) Phenotypic analysis
2) Genotypic analysis
3) Phylogenetic analysis
 Phenotypic analysis examines the morphological,
metabolic, physiological, and chemical characters
of the cell
Some Phenotypic Characteristics of Taxonomic Value
Table 14.3
Some Phenotypic Characteristics of Taxonomic Value
Table 14.3
 Fatty Acid Analyses (FAME: fatty acid methyl ester)
 Relies on variation in type and proportion of fatty acids
present in membrane lipids for specific prokaryotic
groups
 Requires rigid standardization because FAME profiles
can vary as a function of temperature, growth phase,
and growth medium
Fatty Acid Methyl Ester (FAME) Analysis
Figure 14.19a
Fatty Acid Methyl Ester (FAME) Analysis
Figure 14.19b
14.11 Genotypic Analysis
 Several methods of genotypic analysis are
available and used
 DNA-DNA hybridization
 DNA profiling
 Multilocus Sequence Typing (MLST)
 GC Ratio
Some Genotypic Methods Used in Bacterial Taxonomy
 DNA-DNA hybridization
 Genomes of two organisms are hybridized to examine
proportion of similarities in their gene sequences
Genomic Hybridization as a Taxonomic Tool
Figure 14.20a
Figure 14.20b
Figure 14.20c
 DNA-DNA hybridization
 Provides rough index of similarity between two
organisms
 Useful complement to SSU rRNA gene sequencing
 Useful for differentiating very similar organisms
 Hybridization values 70% or higher suggest strains
belong to the same species
 Values of at least 25% suggest same genus
Relationship Between SSU rRNA and DNA Hybridization
97
95
25
70
 DNA Profiling
 Several methods can be used to generate DNA
fragment patterns for analysis of genotypic similarity
among strains, including
 Ribotyping: focuses on a single gene (SSU rRNA)
 Repetitive extragenic palindromic PCR (rep-PCR):
focused on highly conserved repetitive DNA elements
 Amplified fragment length polymorphism (AFLP): focus
on many genes located randomly throughout genome
- digestion of genomic DNA with one or two restriction
enzymes and selective PCR of resulting fragments
DNA Fingerprinting with rep-PCR
Figure 14.22
 Multilocus Sequence Typing (MLST)
 Method in which several different “housekeeping genes”
from an organism are sequenced (~450-bp)
 Has sufficient resolving power to distinguish between
very closely related strains
Multilocus Sequence Typing
 GC Ratios
 Percentage of guanine plus cytosine in an organism’s
genomic DNA
 Vary between 20 and 80% among Bacteria and
Archaea
 Generally accepted that if GC ratios of two strains differ
by ~ 5% they are unlikely to be closely related
14.12 Phylogenetic Analysis
 16S rRNA gene sequences are useful in taxonomy;
serve as “gold standard” for the identification and
description of new species
 Proposed that a bacterium should be considered a new
species if its 16S rRNA gene sequence differs by more
than 3% from any named strain, and a new genus if it
differs by more than 5%
 The lack of divergence of the 16S rRNA gene limits its
effectiveness in discriminating between bacteria at the
species level, thus, a multi-gene approach can be used
 Multi-gene sequence analysis is similar to MLST, but
uses complete sequences and comparisons are made
using cladistic methods
 Whole-genome sequence analyses are becoming
more common
 Provide many traits for comparative genotypic analysis
 Genome structure
- size and number of chromosomes, GC ratio, linear or
circular, etc.
 Gene content
 Gene order
14.13 The Species Concept in Microbiology
 No universally accepted concept of species for
prokaryotes
 Current definition of prokaryotic species
 Collection of strains sharing a high degree of similarity
in several independent traits
 Most important traits include 70% or greater DNA-DNA
hybridization and 97% or greater 16S rRNA gene
sequence identity
Taxonomic Hierarchy for Allochromatium warmingii
 Biological species concept: not meaningful for
prokaryotes as they are haploid and do not undergo
sexual reproduction
 Genealogical species concept: an alternative
 Prokaryotic species is a group of strains that based on
DNA sequences of multiple genes cluster closely with
others phylogenetically and are distinct from other
groups of strains
Multi-Gene Phylogenetic Analysis
16S rRNA genes
gyrB genes
luxABFE genes
50 nucleotide changes
Figure 14.24
 Ecotype
 Population of cells that share a particular resource
 Different ecotypes can coexist in a habitat
 Bacterial speciation may occur from a combination
of repeated periodic selection for a favorable trait
within an ecotype and lateral gene flow
A Model for Bacterial Speciation
Figure 14.25
 This model is based solely on the assumption of
vertical gene flow
 New genetic capabilities can also arise by horizontal
gene transfer
- the extent among bacteria is variable
 No firm estimate on the number of prokaryotic
species
 Nearly 7,000 species of Bacteria and Archaea are
presently known
14.14 Classification and Nomenclature
 Classification
 Organization of organisms into progressively more
inclusive groups on the basis of either phenotypic
similarity or evolutionary relationship
 Prokaryotes are given descriptive genus names and
species epithets following the binomial system of
nomenclature used throughout biology
 Assignment of names for species and higher groups of
prokaryotes is regulated by the Bacteriological Code
- The International Code of Nomenclature of Bacteria
 Major references in bacterial diversity
 Bergey’s Manual of Systematic Bacteriology (Springer)
 The Prokaryotes (Springer)
 Formal recognition of a new prokaryotic species
requires
 Deposition of a sample of the organism in two culture
collections
 Official publication of the new species name and description
in the International Journal of Systematic and Evolutionary
Microbiology (IJSEM)
 The International Committee on Systematics of
Prokaryotes (ICSP) is responsible for overseeing
nomenclature and taxonomy of Bacteria and Archaea
Some National Microbial Culture Collections
KCCM
Korean Culture Center of Microorganisms
Seoul, Korea
http://www.kccm.or.kr
KACC
Korean Agricultural Culture Collection
Suwon, Korea
http://kacc.rda.go.kr
Table 14.6