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Microbiology
14.4.2015
Helmut Pospiech
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Origin and Diversity of Life
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Microbial Diversity
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Origin of Cellular Life
• Early Earth was anoxic and much hotter than
present day (over 100 oC)
• First biochemical compounds were made byabiotic systems that set the stage for the origin of
life
Brock Biology of Microorganisms, 13th ed.
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Origin of Cellular Life
• Surface Origin Hypothesis – Based on Urey-Miller experiment
that tried to simulate conditions onearly earth
– Contends that the first membrane-enclosed, self-replicating cellsarose out of primordial soup rich inorganic and inorganic compoundsin ponds on Earth’s surface
– Dramatic temperature fluctuationsand mixing from meteor impacts,dust clouds, and storms argueagainst this hypothesis
Brock Biology of Microorganisms, 13th ed.
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Origin of Cellular Life
• 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
http://www.ridge2000.org/SEAS/for_students/reference/hydrothermal_vent_intro.html
Submarine hydrothermal vents thatexpell up to 400°C hot, mineral-rich
water form chimneys that are called
black smokers
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Submarine Mound Formed at Ocean Hydrothermal Spring
Figure 14.4
Hot, reduced, alkaline
hydrothermal fluid
Cooler, more oxidized, more
acidic ocean water
Brock Biology of Microorganisms, 12th ed.
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Origin of Cellular Life
• 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 ownsynthesis
Brock Biology of Microorganisms, 12th ed.
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A Model for the Origin of Cellular Life
Last Universal Common Ancestor
Brock Biology of Microorganisms, 13th ed.
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An alkaline hydrothermal vent
harbours a natural proton gradient
The flux of hydrothermal effluent maintains an
alkaline interior. In the presence of appropriate
proteins, this source of energy could, in principle, be
tapped. The harnessing of naturally preexisting
chemiosmotic gradients before the advent of
genetically specified mechanisms to generate such
gradients would directly explain why ATP synthases of
the F-type (eubacteria) and A-type (archaebacteria)
are universal and conserved, but the mechanisms to
generate proton gradients are not.
Martin Biology Direct 2011 6:36 doi:10.1186/1745-
6150-6-36
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Origin of Cellular Life
• DNA, a more stable molecule, eventually becamethe genetic repository
• Three-part systems (DNA, RNA, and protein)evolved and became universal among cells
èDNA may have been invented by viruses as an
mechanism to evade host responseè current viruses also utilise modified bases for the
same reason
Brock Biology of Microorganisms, 12th ed.
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Brock Biology of
Microorganisms,13th ed.
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A model for the transfer of DNA from viruses to cells for
the origin of cellular DNA chromosomes and plasmidA DNA virus (DNA genome in red) infected
an RNA-cell (RNA genome in blue) (A) and
co-evolved with it in a carrier state (B).Genes from the cellular RNA genomes are
progressively transferred to the viral DNA
genome by retrotranscription (white
arrow) and the viral genome evolved into
a DNA plasmid of the RNA-cell (C). The
DNA plasmid finally out-competed the
RNA genome and become a cellular DNA
chromosome (D). Infection of a DNA cell
by a DNA virus can led, by a similarmechanism, to a DNA cell with both a
plasmid and a chromosome (E–G). This
scenario should produce a procaryotic
type of cell. For the formation of
eukaryotic cells, the nucleus could have
originated by viral-induced recruitment of
intracellular membranes to produce the
nuclear membrane, by
a mechanism derived from the processused by large double-stranded DNA
viruses to form their envelopes.
Forterre P. (2005) The two ages of the RNA world, and the transition tothe DNA world: a story of viruses and cells. Biochimie 87, 793-803.
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Koonin EV, Senkevich TG, Dolja VV. (2006) The
ancient Virus World and evolution of cells. Biol
Direct 1, 29.
A Model for the Origin of Cellular Life• Viruses may have large
impact on thedevelopment of life(Eugen Koonin andPatrick Forterre)
• Evidence for multiple
viral lines already at thetime of LUCA
• Probably, there existedtwo types of early “lifeforms”: capsid-engulfed
(viruses) und lipidmembrane engulfed(cellular) life
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Origin of Cellular Life
• Other Important Steps in Emergence of Cellular Life
– Build up of lipids
– Synthesis of phospholipid
membrane vesicles thatenclosed the cell’s
biochemical and replication
machinery
• May have been similar to montmorillonite clay
vesicles
Lipid Vesicles Made in the
Laboratory from Myristic Acid
Vesicles formed on Montmorillonite clay particles
Brock Biology of Microorganisms, 12th ed.
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Origin of Cellular Life
• 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
Brock Biology of Microorganisms, 12th ed.
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Energy Metabolism of the First Free
Cells• After establishment of a
cytoplasma membraneand the release of firstcells from theclay/serpentine mounds,the cell had to be able toestablish an own schemeto produce a protongradient
• Possible as ironchemolithotrophs using a
primitive hydrogenase
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Origin of Cellular Life
• 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
Brock Biology of Microorganisms, 12th ed.
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MICROBIAL DIVERSIFICATION
PART II.
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Microbial Diversification
• Molecular evidence suggests ancestors of
Bacteria and Archaea diverged ~ 4 billion
years ago
• As lineages diverged, distinct metabolisms
developed
• Development of oxygenic photosynthesisdramatically changed course of evolution
Brock Biology of Microorganisms, 12th ed.
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Microbial Diversification
• ~ 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
Brock Biology of Microorganisms, 12th ed.
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Banded Iron Formations
Figure 14.9
Iron oxides
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Brock Biology of Microorganisms, 12th ed.
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Microbial Diversification
• Development of oxic atmosphere led to evolution of new metabolic pathways that yielded more energythan anaerobic metabolisms
• Consequence of O2 for the evolution of life
– Formation of ozone layer that provides a barrier against UVradiation• Without this ozone shield, life would only have continued
beneath ocean surface and in protected terrestrialenvironments
• Oxygen also spurred evolution of organelle-containing
eukaryotic microorganisms – Oldest eukaryotic microfossils ~ 2 billion years old
– Fossils of multicellular and more complex eukaryotes arefound in rocks 1.9 to 1.4 billion years old
Brock Biology of Microorganisms, 12th ed.
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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
Brock Biology of Microorganisms, 12th ed.
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Endosymbiotic Origin of Eukaryotes• Different hypotheses exist to explain the formation of
the eukaryotic cell1) Eukaryotes began as nucleus-bearing lineage that later
acquired mitochondria and chloroplasts by endosymbiosis
Brock Biology of Microorganisms, 13th ed.
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Endosymbiotic Origin of Eukaryotes• Different 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 tomitochondria and an archaean host
Brock Biology of Microorganisms, 13th ed.
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Endosymbiotic Origin of Eukaryotes
• Both hypotheses suggest eukaryotic cell is
chimeric
• This is supported by several features
– Eukaryotes have similar lipids and energy metabolismsto Bacteria
– Eukaryotes have transcription and translational
machinery most similar to Archaea
• But neither of the two hypotheses explains
how the nucleus itself evolved!!!
Brock Biology of Microorganisms, 12th ed.
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The Viral Eukaryogenesis Hypothesis
• Many large viruses such as poxvirusesreplicate their DNA in the cytoplasm inmembrane-engulfed compartments
• Poxvirus-related virus that infectArchaea are known
Bell PJ (2009) The viral eukaryogenesis hypothesis: a key role for viruses in the
emergence of eukaryotes from a prokaryotic world environment. Ann N Y Acad Sci1178, 91-105.
Condit (2007) Cell Host & Microbe 2, 205 - 207
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Viruses and other selfish
genetic elements may
have contributed inmany ways to the
development of the
eukaryotic cell
Koonin EV, Senkevich TG, Dolja VV. (2006) The ancient Virus
World and evolution of cells. Biol Direct 1, 29.
• Nucleus and part of the
nuclear replication apparatus
• Mitochondrial DNAreplication apparatus
• introns
• (retro-)transposons
• etc.
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A new fusion hypothesis for the origin of Eukarya:
better than previous ones, but probably also wrong
Fig. 2. The PTV fusion hypothesis based on the engulfment of a thaumarchaeon by a PVC bacterium followed by viral
invasions. Bacterial and archaeal membranes, cytoplasmic and nuclear components (including circular chromosome) are in
green and purple, respectively. Eukaryal cytoplasmic and nuclear components are in grey to symbolize differences with
their archaeal ancestors. Eukaryal chromosomes (linear) are in orange. Abbreviations are as in Fig. 1. ICM: Intracytoplasmic
membrane. NE: nuclear envelope. PVC: Planctomycetes, Verrucomicrobia, Chlamydiae superphylum. For simplicity thereticulum endoplasmicmembrane deriving from the ICM of the PVC bacterium has not been indicated.
P. Forterre (2011) Research in
Microbiology 162, 77e91
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Forterre P (2013)The common
ancestor of archaea and
eukarya was not an archaeon.Archaea 2013:372396.
Fusion or
not fusion –
that is thequestion
here!
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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 geneduplication, horizontal gene transfer, and
gene loss
Brock Biology of Microorganisms, 12th ed.
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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
Brock Biology of Microorganisms, 12th ed.
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Evolutionary Analysis: Theoretical
Aspects
• 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
Brock Biology of Microorganisms, 12th ed.
Ribosomal RNA
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Ribosomal RNA
Figure 14.11
16S rRNA
from E. coli
Brock Biology of Microorganisms, 12th ed.
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Evolutionary Analysis: Theoretical
Aspects
• 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
Brock Biology of Microorganisms, 12th ed.
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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
Brock Biology of Microorganisms, 13th ed.
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Evolutionary Analysis: Analytical Methods
• 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
Brock Biology of Microorganisms, 13th ed.
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Evolutionary Analysis: Analytical
Methods
• 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 informativeand define monophyletic groups (a group which contains
all the descendants of a common ancestor; a clade)
Brock Biology of Microorganisms, 12th ed.
l l l l h d
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Evolutionary Analysis: Analytical Methods
• Common cladistic methods
– Parsimony
– Maximum likelihood
– Bayesian analysis
Identification of Phylogenetically Informative Sites
Figure 16.15
Dots: neutral sites.
Arrows: phylogenetically informative sites.
Brock Biology of Microorganisms, 13th ed.
Universal Phylogenetic Tree as Determined by rRNA Genes
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Universal Phylogenetic Tree as Determined by rRNA Genes
Brock Biology of Microorganisms, 13th ed.
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Microbial Phylogeny
• Domain Archaea consists of two major groups – Crenarchaeota
– Euryarchaeota
• 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
Brock Biology of Microorganisms, 13th ed.
Each of the three domains of life can be
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Each of the three domains of life can be
characterized by various phenotypic properties
Brock Biology of Microorganisms, 13th ed.
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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
Brock Biology of Microorganisms, 13th ed.
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Phenotypic Analysis
• Bacterial taxonomy incorporates multiple methodsfor identification and description of new species
• The polyphasic approach to taxonomy uses three
methods
1) Phenotypic analysis
2) Genotypic analysis
3) Phylogenetic analysis
Brock Biology of Microorganisms, 13th ed.
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Phenotypic analysis examines the
morphological, metabolic, physiological, and
chemical characters of the cell
Brock Biology of Microorganisms, 13th ed.
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Genotypic Analysis
• Several methods of genotypic analysis areavailable and used – DNA-DNA hybridization
– DNA profiling
– Multilocus Sequence Typing (MLST) or whole genomesequencing
– GC Ratio
Brock Biology of Microorganisms, 13th ed.
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Genotypic Analysis
• DNA-DNA hybridization – Genomes of two organisms are hybridized to examine
proportion of similarities in their gene sequences
Brock Biology of Microorganisms, 12th ed.
Genomic Hybridization as a Taxonomic Tool
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Genomic Hybridization as a Taxonomic Tool
Figure 14.20a
Brock Biology of Microorganisms, 12th ed.
Genomic Hybridization as a Taxonomic Tool
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Genomic Hybridization as a Taxonomic Tool
Figure 14.20b
Brock Biology of Microorganisms, 12th ed.
Genomic Hybridization as a Taxonomic Tool
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Genomic Hybridization as a Taxonomic Tool
Figure 14.20c
Brock Biology of Microorganisms, 12th ed.
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Phylogenetic Analysis
• 16S rRNA gene sequences are useful intaxonomy; 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 morethan 3% from any named strain, and a new genus if it
differs by more than 5%
Brock Biology of Microorganisms, 12th ed.
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Phylogenetic Analysis
• Whole-genome sequence analyses are becoming
more common
– Genome structure; size and number of chromosomes,
GC ratio, etc. – Gene content
– Gene order
Brock Biology of Microorganisms, 12th ed.
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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
Brock Biology of Microorganisms, 12th ed.
Taxonomic Hierarchy for Allochromatium warmingii
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y g
Brock Biology of Microorganisms, 13th ed.
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The Species Concept in Microbiology
• Biological species concept not meaningfulfor prokaryotes as they are haploid and do
not undergo sexual reproduction
• Genealogical species concept is analternative – 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
Brock Biology of Microorganisms, 12th ed.
Mult i-Gene Phylogenetic Analysis
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y g y
Figure 14.24
16S rRNA genes
gyrB genes
luxABFE genes
Brock Biology of Microorganisms, 12th ed.
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The Species Concept in Microbiology
• Ecotype
– Population of cells that share a particular resource
– Different ecotypes can coexist in a habitat
• Bacterial speciation may occur from acombination of repeated periodic selection for a
favorable trait within an ecotype and lateral gene
flow
Brock Biology of Microorganisms, 12th ed.
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The Species Concept in Microbiology
• This model is based solely on the
assumption of vertical gene flow
• New genetic capabilities can also arise byhorizontal gene transfer; the extent among
bacteria is variable
Brock Biology of Microorganisms, 12th ed.
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Trouble with the Tree of Life Concept
”Ring of Life” rather than a ”tree of life”
since the eukaryotic genome represents a
fusion of a bacterial and archaeal genome
(Riviera and Lake (2004), Nature 431, 152)
A reticulated tree would better describe the
genotypic relationship of organisms due to
vast horizontal gene transfer
(Doolittle (1999), Science 284, 2124; Martin
(1999), BioEssays 21, 99)
Universal common ancestry
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Universal common ancestry
of life on earth?
a, The multiple-ancestry possibility: depicted here is life originating from two separate forms,
with proteins with similar functions arising independently. Transfers, by endosymbiosis or by
lateral gene transfers, are shown by dotted lines. b, A single origin (universal common
ancestry), at least after the advent of protein synthesis. Correlations between patterns at
different amino-acid positions are used to test between the two possibilities.
Steel M & Penny D (2010) Nature 465,168.
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The Species Concept in Microbiology
• No firm estimate on the number of prokaryotic
species
• Nearly 7,000 species of Bacteria and Archaea arepresently known
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Classification and Nomenclature
• Classification
– Organization of organisms into progressively more
inclusive groups on the basis of either phenotypic
similarity or evolutionary relationship
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Classification and Nomenclature
• Prokaryotes are given descriptive genusnames and species epithets following thebinomial system of nomenclature usedthroughout biology
• Assignment of names for species and higher groups of prokaryotes is regulated by the
Bacteriological Code- The International Code of Nomenclature of Bacteria
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14.14 Classification and Nomenclature
• Major references in bacterial diversity
– Bergey’s Manual of Systematic Bacteriology (Springer)
– The Prokaryotes (Springer)
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Classification and Nomenclature
• 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