Download Freeman 1e: How we got there

CHAPTER 11
Microbial Evolution and Systematics
Early Earth, the Origin off Life,
and Microbial Diversification
• Planet Earth is approximately 4.6 billion
years old. The first evidence for microbial life
can be found in rocks about 3.86 billion years
old.
• Stromatolites are fossilized microbial mats
consisting of layers of filamentous prokaryotes
and trapped sediment.
• By comparing ancient stromatolites with modern
stromatolites, it has been concluded that filamentous
phototrophic bacteria, perhaps relatives of the green
nonsulfur bacterium Chloroflexus, formed ancient
stromatolites.
• Early Earth was anoxic and much hotter than the
present Earth. The first biochemical compounds were
made by abiotic syntheses that set the stage for the
origin of life.
Primitive Life: The RNA World
and Molecular Coding
• The first life forms may have been self-replicating
RNAs (RNA life). These were both catalytic and
informational. Eventually, DNA became the genetic
repository of cells, and the three-part system—DNA,
RNA, and protein—became universal among cells
(Figure 11.5).
Possible mechanileifsm of evolution of life
Primitive Life: Energy and
Carbon Metabolism
• Primitive metabolism was anaerobic and
likely chemolithotrophic, exploiting the
abundant sources of FeS and H2S present
(Figure 11.6). Carbon metabolism may have
included autotrophy.
Energy generating scheme for primitive cell
• Oxygenic photosynthesis led to development of
banded iron formations, an oxic environment, and
great bursts of biological evolution (Figure 11.8).
Landmarks of biological evolution
Eukaryotes and Organelles:
Endosymbiosis
• The eukaryotic nucleus and mitotic apparatus
probably arose as a necessity for ensuring the orderly
partitioning of DNA in large-genome organisms.
• Mitochondria and chloroplasts, the principal energyproducing organelles of eukaryotes, arose from the
symbiotic association of prokaryotes of the domain
Bacteria within eukaryotic cells, a process called
endosymbiosis (Figure 11.9).
• Mitochondria arose from
the Proteobacteria, a
major group of Bacteria.
• Origin of the modern life
• Assuming that an RNA world existed, selfreplicating entities have populated Earth for
over 4 billion years (Figure 11.10).
Self replicating entities
on earth
Methods for Determining
Evolutionary Relationships,
Evolutionary Chronometers,
• The phylogeny of microorganisms is their
evolutionary relationships.
• Certain genes and proteins are evolutionary
chronometers—measures of evolutionary
change. Comparisons of sequences of
ribosomal RNA can be used to determine the
evolutionary relationships among organisms.
• SSU (small subunit) RNA sequencing is
synonymous with 16S or 18S sequencing.
• Differences in nucleotide or amino acid sequence of
functionally similar (homologous) macromolecules are
a function of their evolutionary distance.
• Phylogenetic trees based on ribosomal RNA have
now been prepared for all the major prokaryotic and
eukaryotic groups.
• A huge database of rRNA sequences exists. For
example, the Ribosomal Database Project (RDP)
contains a large collection of such sequences, now
numbering over 100,000.
Ribosomal RNA Sequences as a
Tool of Molecular Evolution
• Comparative ribosomal RNA sequencing (Figure
11.11) is now a routine procedure involving the
amplification of the gene encoding 16S ribosomal
RNA, sequencing it, and analyzing the sequence in
reference to other sequences (Figure 11.12).
Ribosomal RNA
rRNA sequencing
• Two major treeing algorithms are distance and
parsimony (Figure 11.13).
Signature Sequences, Phylogenetic Probes,
and Microbial Community Analyses
• Signature sequences, short oligonucleotides
found within a ribosomal RNA molecule, can
be highly diagnostic of a particular organism
or group of related organisms. Table 11.1
shows signature sequences from 16S or 18S
rRNA defining the three domains of life.
• Signature sequences can be used to generate
specific phylogenetic probes, useful for
fluorescent in situ hybridization (FISH) or
microbial community analyses.
Microbial Evolution
Microbial Phylogeny Derived
from Ribosomal RNA
Sequences
• The universal phylogenetic tree (Figure
11.16) is the road map of life.
Universal phylogenetic tree
• Life on Earth evolved along three major
lines, called domains, all derived from a
common ancestor.
•Each domain contains several phyla.
•Two of the domains, Bacteria and Archaea,
remained prokaryotic, whereas the third,
Eukarya, evolved into the modern eukaryotic
cell.
Characteristics of the Domains of Life
• Although the three domains of living organisms were
originally defined by ribosomal RNA sequencing,
subsequent studies have shown that they differ in
many other ways.
• In particular, the Bacteria and Archaea differ
extensively in cell wall and lipid chemistry (Figure
11.18) and in features of transcription and protein
synthesis (Table 11.2).
Lipids in cell wall
• Table 11.3 summarizes a number of other phenotypic
features, physiological and otherwise, that can be used
to differentiate organisms at the domain level.
Microbial Taxonomy And Its
Relationship To Phylogeny
Classical Taxonomy
• Conventional bacterial taxonomy places
heavy emphasis on analyses of phenotypic
properties of the organism (Table 11.4).
• To identify an organism, one must assess
several of its phenotypic properties, from
general to specific (Figure 11.20).
• Determining the guanine plus cytosine base
ratio (GC ratio) of the DNA of the organism
can be part of this process (Figure 11.21).
Chemotaxonomy
• Molecular taxonomy involves molecular
analyses of specific cell components.
• These include, among others, DNA:DNA
hybridization (Figure 11.22), ribotyping and
multilocus sequence typing (MLST) (Figure
11.23), and fatty acid analyses, such as fatty
acid methyl ester (FAME) analysis (Figure
11.24).
Genomic hybridization as taxonomic tool
Ribotyping
Multilocus sequence typing
Fatty acid methyl ester (FAME) analysis
• Genomic hybridization measures the
degree of sequence similarity in two DNAs
and is useful for differentiating very closely
related organisms where rRNA sequencing
may not be definitive.
The Species Concept in Microbiology
• The species concept applies to prokaryotes
as well as eukaryotes, and a similar
taxonomic hierarchy exists.
• Groups of genera (singular: genus) are
collected into families, families into orders,
orders into classes, classes into phyla
(singular: phylum), and so on up to the
highest-level taxon, the domain.
• It has been proposed that a prokaryote
whose 16S ribosomal RNA sequence differs
by more than 3% from that of all other
organisms (that is, the sequence is less than
97% identical to any other sequence in the
databases), should be considered a new
species (Figure 11.25).
Relationship between 16S ribosomal RNA sequence similarity and
genomic DNA:DNA hybridization
• Bacterial speciation may occur from a
combination of repeated periodic selection for
a favorable trait within an ecotype and lateral
gene flow (Figure 11.26).
A model for bacterial
speciation
• The model for speciation shown is based
solely on the assumption of vertical (mother
to daughter) gene flow. However, bacterial
speciation is also affected to some degree by
lateral (horizontal) gene transfer. Lateral
flow is the transfer of genes between species
by conjugation, transduction, and
transformation.
• Table 11.5 gives the taxonomic hierarchy for the
purple sulfur bacterium Allochromatium warmingii.
• Table 11.6 lists taxonomic ranks and
numbers of known prokaryotic species.
Nomenclature and Bergey's
Manual
• Following the binomial system of
nomenclature used throughout biology,
prokaryotes are given descriptive genus
names and species epithets.
• Formal recognition of a new prokaryotic
species requires deposition of a sample of the
organism in a culture collection and official
publication of the new species name and
description. Bergey's Manual of Systematic
Bacteriology is a major taxonomic
compilation of Bacteria and Archaea.