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

Figure 14.1

3.45 billion-year-old rocks, South Africa

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

Figure 14.2

3.5 billion yrs oldOldest (Western Australia)

1.6 billion yrs old(Northern Australia)

Modern stromatolites(Western Australia)

Modern stromatolites(Yellow Stone NP)

Modern stromatolites(Western Australia)

More Recent Fossil Bacteria and Eukaryotes

Figure 14.3

From 1 billion yrs old rocks in Central Australia

Prokaryotes (bacteria) Eukaryotic cells

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, 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 vesicles synthesized on the

surfaces of montmorillonite clay

Lipid Vesicles Made in the Laboratory from Myristic Acid

Figure 14.6

RNAs

vesicle

Vesicle synthesis is catalyzed by the surfaces of 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 (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

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

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

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

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

Figure 14.15

Dots: neutral sites.Arrows: phylogenetically informative sites, varying in at least two of the sequences.

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

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

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

Figure 14.24

16S rRNA genesgyrB genesluxABFE genes

50 nucleotide changes

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

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