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Microbial
Diversity
Miftahul Ilmi
19/02/2018
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MICROBIAL
EVOLUTION AND
THREE OF LIFE
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History of Earth: Overview

• 4.5 BYA: Earth formed

• 4 BYA: Cellular life started
• 3.5 BYA: First
photosynthesis
• 1.5 BYA: First multicellular
eukaryotes
• 0.5 BYA: Cambrian
explosion
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Origin of Cellular Life

• Still a great mysteries
• Earth surface was too
hostile, life originated
at hydrothermal
springs
• Hydrothermal springs
provided energy and
nutrients for life
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Origin of Cellular Life

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Origins of Eukaryotes

Nucleated Line: Hydrogen hypothesis:

• Archaea formed nucleus • Symbiosis between H2 producing
• Nucleated cell acquired mitochondria Bacteria with H2 consuming Archaea
and chloroplast by endosymbiosis • Nucleus formed after symbiosis
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Tree of Life: Ernst Haeckel 1866

• Single cell organisms
(Monera) were ancestor of
other organisms
• Only included plants,
protists, and animals in the
scheme
• Evolutionary relationship
between microorganisms
was not resolved
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Tree of Life: Robert Whittaker 1967

• The five kingdoms
system
• Fungi a distinct
lineage
• Evolutionary
relationship between
microorganisms still
unsolved
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Domain of Life: Carl Woese 1977

• Universal phylogenetic tree as determined from comparative SSU

rRNA gene sequence analysis.
• At least 84 phyla of Bacteria have now been identified although
many of these have not yet been cultured.
• LUCA: last universal common ancestor.
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Bacteria vs Archaea vs Eukarya

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Taxonomic Methods in Microbial Systematics

• Microbial species concepts:

– all members of a species should be genetically and phenotypically
cohesive
– their traits should be distinct from those described for other species
– a species should be monophyletic: the strains composing the species
should all share a recent common ancestor to the exclusion of other
species
• For Bacteria and Archaea, species are defined operationally as a
group of strains sharing a high degree of similarity in many traits
and sharing a recent common ancestor for their 16S rRNA genes.
• A value of 70% or less DNA-DNA hybridization and a difference in
16S rRNA gene sequence of 3% or more between two organisms is
taken as evidence that the two are distinct species.
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DIVERSITY OF
BACTERIA
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Proteobacteria
• Largest group of Bacteria (1/3 of
described species)
• All gram negative
• Energy-generating mechanisms:
chemolithotrophic,
chemoorganotrophic, phototrophic
• Relation to oxygen: anaerobic,
microaerophilic, and facultatively
aerobic
• Cell shapes: straight and curved rods,
cocci, spirilla, filamentous, budding,
and appendaged forms
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Proteobacteria
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Proteobacteria
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Firmicutes, Tenericutes, and Actinobacteria

• All members are gram positive

• Actinobacteria:
– high GC content
– filamentous bacteria
• Firmicutes:
– Low GC content
– endospore forming bacteria, lactic
acid bacteria
• Tenericutes:
– Lack of cell walls: mycoplasma
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Bacteroidetes
• Gram negative
• Non-sporulating rods
• Saccharolytic
• Also can be aerobic or
fermentative
• Major species has
gliding motility
• Major component of
microbial community in
human gut
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Chlamydiae, Planctomycetes, and Verrucomicrobia

• Chlamydiae: obligate intracellular

parasites of eukaryotes.
• Planctomycetes:
– gram-negative bacteria
– many divide by budding
– often have stalks or appendages
– cells arranged in rosettes
– cell wall lack peptidoglycan
– intercellular compartments
• Verrucomicrobia:
– aerobic or facultative aerobic
– capable of fermenting sugars
– some form symbiosis with protists
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DIVERSITY OF
ARCHAEA
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Spang et al., Trends in Microbiology 18: 8 (2010)

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Euryarchaeota
• Extremely halophilic
– Halobacterium, Haloferax, Natronobacterium
• Methanogenic
– Methanobacterium, Methanocaldococcus, Methanosarcina
• Thermophilic and extremely acidophilic
– Thermoplasma, Picrophilus, Ferroplasma
• Hyperthermophilic
– Thermococcus,Pyrococcus, Methanopyrus
• Hyperthermophilic, anaerobic respiration using sulfur
– Archaeoglobus, Ferroglobus
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Scanning electron micrographs of cells of diverse species of methanogenic Archaea. (a)

Methanobrevibacter ruminantium. A cell is about 0.7 μm in diameter. (b) Methanobrevibacter
arboriphilus. A cell is about 1 μm in diameter. (c) Methanospirillum hungatei. A cell is about 0.4
μm in diameter. (d) Methanosarcina barkeri. A cell is about 1.7 μm wide.
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Thaumarchaeota, Nanoarchaeota, and

Korarchaeota
• Thaumarchaeota
– Nitrosopumilus, Nitrososphaera
– Nitrification archaea
• Nanoarchaeota
– Nanoarchaeum
– Parasites of Ignicoccus hospitalis, another archaea
• Korarchaeota
– Korarchaeum
– obligate anaerobic chemoorganotroph,
hyperthermophile, filament-shaped cell
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Nanoarchaeum equitans. (a)Fluorescence micrograph of cells of N.

equitans(red) attached to cells of Ignicoccus(green). (b)Transmission
electron micrograph of a thin section of a cell of N. equitans.
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Crenarchaeota
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Desulfurococcales with growth temperature optima >100°C. (a) Pyrodictium occultum (growth
temperature optimum, 105°C), dark-field micrograph. (b) Thin-section electron micrograph of P.
occultum. Cells are highly variable in diameter from 0.3 to 2.5 μm. (c) Thin section of a cell of Pyrolobus
fumarii, one of the most thermophilic of all known bacteria (growth temperature optimum, 106°C); a
cell is about 1.4 μm in diameter. (d) Negative stain of a cell of “Strain 121,” capable of growth at 121°C;
a cell is about 1 μm wide.
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DIVERSITY OF
MICROBIAL
EUKARYOTE
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Protists
• Euglenozoans
– Kinetoplastids (Trypanosoma)
– Euglenids (Euglena)
• Alveolates (alveoli - cytoplasmic sacs under
cytoplasmic membrane)
– Ciliates (Paramecium)
– Dinoflagellates (Gonyaulax)
– Apicomplexans (Toxoplasma, Plasmodium)
• Stramenopiles
– Diatoms
– Oomycetes
– Golden Algae and Brown Algae
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Protists
• Cercozoans and Radiolarians
– Cercozoa
– Radiolaria (foraminifera)
• Amoebozoa
– Gymnamoebas and Entamoebas (Amoeba,
Entamoeba)
– Slime Molds
• Diplomonads and Parabasalids
– Diplomonads (Giardia)
– Parabasalids (Trichomonas)
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Paramecium
Euglena

Diatoms
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Fungi
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Fungi
• Chytridiomycetes
– Most primitive fungi, flagellated sexual spores
• Zygomycetes and Glomeromycetes
– Rhizophus, Microsporidia
– Coenocytic, zygospores
– glomeromycetes: mycorrhizal associations
• Ascomycetes
– Saccharomyces, Candida, Aspergillus
– Sexual spore: ascospores, asexual spores: conidia
• Basidiomycetes (mushroom)
– Agaricus, Amanita
– Sexual spore: basidiospore
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Ascomycetes

Zygomycetes Microsporidia Basidiomycetes

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Red and Green Algae

• Red Algae (rodhophytes)
– Polysiphonia, Cyanidium, Galdiera
– Contain chlorophyll a, phycoerythrin,
phycobiliproteins
• Green Algae
– Chlamydomonas,Volvox
– Chloroplasts containing chlorophylls a and b
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Green algae
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