ch14 장 ppt

Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Brock Biology of Microorganisms

Twelfth Edition

Madigan / Martinko

Dunlap / Clark

Microbial Evolution and Systematics

Cha

pter

14

Lectures by Buchan & LeCleir


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



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

Figure 14.1

3.45 billion-year-old rocks, South Africa



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

Figure 14.2

3.5 billion yrs old 1.6 billion yrs old


More Recent Fossil Bacteria and Eukaryotes

Figure 14.3

1 billion yrs old rocks

prokaryotes

eukaryotic cells



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, self-

replicating 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

Figure 14.4

Hot, reduced, alkaline hydrothermal fluid

Cooler, more oxidized, more acidic ocean water



Prebiotic chemistry of early Earth set stage for self-

replicating systems

First self-replicating systems may have been RNA-

based (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

Figure 14.5

Last Universal Common Ancestor



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 montmorillonite clay vesicles


Lipid Vesicles Made in the Laboratory from Myristic Acid

Figure 14.6

RNAs

vesicle

Vesicles formed on Montmorillonite clay particles



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 in the oceans (i.e., FeS, FeS2)

Banded iron formations: laminated sedimentary rocks;

prominent feature in geological record


Banded Iron Formations

Figure 14.9

Iron oxides



Development of oxic atmosphere led to evolution of

new metabolic pathways that yielded more energy

than anaerobic metabolisms



Oxygen also spurred evolution of organelle-

containing 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



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


Models for the Origin of the Eukaryotic Cell

Figure 14.10a



Two hypotheses exist to explain the formation of

the eukaryotic cell (cont’d)

2) Eukaryotic cell arose from intracellular association

between O2-consuming bacterium (the symbiont),

which gave rise to mitochondria and an archaean host


Models for the Origin of the Eukaryotic Cell

Figure 14.10b



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



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

Figure 14.11

16S rRNA from E. coli



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



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

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

Figure 14.15

Dots: neutral sites.

Arrows: phylogenetically informative sites.



Common cladistic methods

Parsimony

Maximum likelihood

Bayesian analysis



The universal phylogenetic tree based on SSU rRNA

genes is a genealogy of all life on Earth

Animation: Generating Phylogenetic TreesAnimation: Generating Phylogenetic Trees


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

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


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

Figure 14.17

Stained with universal rRNA probe

Stained with a eukaryotic rRNA probe



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



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



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



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




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




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

Figure 14.21

97

95

25



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

Repetitive extragenic palindromic PCR (rep-PCR)

and Amplified fragment length polymorphism

(AFLP): focus on many genes located randomly

throughout genome


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



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

Genome structure; size and number of chromosomes,

GC ratio, etc.

Gene content

Gene order



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 is 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

Figure 14.24

16S rRNA genes

gyrB genes

luxABFE genes



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



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

Table 14.6

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

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