7- Taxonomy of Bacteria

Question 1

What are the 3 components of taxonomy?

Answer 1

Nomenclature (naming), classification(group) and identification(characteristics)

Question 2

What is nomenclature?

What are the 2 names of an organisms?

Answer 2

• Binomial system developed by Carl Linnaeus (1707 -1778) is
used to name all cellular organisms, including microorganisms.

• Each organism is given two names:
– A generic name (genus)
– A specific name (species)

Question 3

Classification- 2 branches

What is a species?

Answer 3

• Overall similarities (Phenetic)
• Evolutionary relationships (Phylogenetic)

Plants, animals and organisms that are capable of sexual reproduction: a species is a group of organisms that can interbreed.

Question 4

What are stromatolites?

Comparison with ancient and modern?

Answer 4

• Stromatolites: Microbial mats consisting of layers of filamentous prokaryotes, sediments and extracellular matrix.

• Similar structure found in rocks 3.5
billion years old or younger.

• Comparison of ancient and modern stromatolites:
– Anoxygenic phototrophic
filamentous bacteria formed ancient stromatolites

– Oxygenic phototrophic
cyanobacteria dominate modern stromatolites

Question 5

Origin of cellular life; surface origin hypothesis; subsurface origin hypothesis

Answer 5

• Early Earth was anoxic and much hotter than present day
– First biochemical compounds were made by abiotic systems that set the stage for the origin of life

• Surface origin hypothesis
– 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 (day/night) and mixing from meteor impacts, dust clouds, and storms argue against this hypothesis

• Subsurface origin hypothesis
– Life originated in hydrothermal springs on the ocean floor
– Conditions would have been more stable
– Steady and abundant supply of energy (e.g., H2 and H2S) was likely available at these
sites

Question 6

What is horizontal gene transfer?

Answer 6

Exchange of genetic material btw cells

Question 7

Origin of cellular life- started with…? And then 3 parts…? Other important steps? Whats is LUCA?

Answer 7

• Prebiotic chemistry of early Earth set the stage for self-replicating systems.

• First self-replicating system 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 (Ribozymes).
– RNA can be copied like DNA.

• 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 the emergence of cellular life
– Buildup of lipids
– Synthesis of phospholipid membrane vesicles
– Assembly of vesicles catalyzed by the clay of the mound, produce cytoplasmic membrane.

• Last universal common ancestor (LUCA): population of early cells from which
cellular life may have diverged into ancestors of modern-day Bacteria and Archaea.

Question 8

When earth was anoxic; energy-generating metabolisms. C source; E and e source;

Answer 8

• As early Earth was anoxic, energy-generating metabolism of primitive cells was exclusively anaerobic and likely chemoautotrophic.
• Carbon source: CO2; Energy and electrons source: H2 likely generated by H2S reacting with FeS (2 compounds present in hydrothermal mounds).

Question 9

What first supported the production of large amounts of organic compounds?

Answer 9

Chemoautotrophic and photoautotrophic metaboliism

Organic material provided an
abundant, diverse, and continually renewed source of reduced organic carbon, stimulating evolution of
various chemoheterotrophic
metabolisms

• Metabolic diversification, colonization of other niches…

Question 10

Classification; Phenetic and phylogenetic

Answer 10

Phenetic: morphology, physiology, biochemestry

Phylogenetic: Fossil record, ribosomal RNA sequences, multi-locus sequences typing, whole genome sequencing

Question 11

Phenetic: numerical taxonomy- what is it? What is a Phenon?

Answer 11

Traditional method for the classification of prokaryotes introduced 200 years ago
by Michael Adanson.

– All characteristics should be considered to be of equal importance (unbiased).
– Classification should be base on as many features as possible.
– Organisms should be grouped on the basis of overall similarity.

Phenon: group of organisms that have characters in common.

Question 12

What is the evolutionary process?

Answer 12

• A mutation is a change in the genome of an organism (nucleotide change,
insertion, deletion).
• Gene duplication, gene loss and horizontal gene transfer (acquisition of a whole new gene from another organism).
• Genetic change may be silent, deleterious or beneficial (new function or change in activity).
• Evolutionary pressure (stress) selects or discards mutation.
– Adaptive mutations improve fitness of an organism, increasing survival in its
environment.
– Silent mutations may be beneficial in other environments allowing the microorganism to
colonize new niches.
– Deleterious mutation is usually lost.
– Accumulation of mutations may lead to speciation (rise of a new species).

Question 13

Phylogenetic- Who? What?

Answer 13

Sequencing ribosomal RNA

• Carl Woese (1970s):
– Sequencing of the small subunit rRNA (SSU rRNA):
16S rRNA in prokaryotes, 18S rRNA in eukaryotes.
– Established the presence of three domains of life:
Bacteria, Archaea, and Eukarya
– Provided a unified phylogenetic framework for
Bacteria

• Comparative rRNA sequencing is a routine
procedure that involves the following:
– Amplification of the gene encoding SSU rRNA
– Sequencing of the amplified gene
– Analysis of sequence in reference to other sequences

• rRNA sequencing is used to infer the phylogeny of prokaryotes and other microorganisms.

Question 14

What is SSU rRNA?

Answer 14

Structure of 16S rRNA & Align sequences (to take into account insertion/deletion)
Conserved region and variable
region (colored).

Accumulation of neutral mutation through time (genetic drim).
The evolutionary relationship
between two organisms is directly correlated to the number of mutation that have accumulated in each one.

Few differences: closely related
(e.g. E. coli and Salmonella)
Many differences: diverge a long time ago (e.g. Bacteria and
Archaea).

Question 15

Phylogenetic tree; how to construct?

Answer 15

Construct phylogenetic trees: graphic illustration of the relationships among sequences

– Branch length represents the number of changes that have occurred along that branch (usually a scale is included)
– Branches define the order of descent and ancestry of the nodes
– Nodes: putative common ancestor.

Question 16

Endosymbiotic origin of Eukaryotes; hypothesis

Answer 16

Endosymbiosis is a well-supported hypothesis for the origin of eukaryotic cells

• Implies that mitochondria and chloroplasts arose from symbiotic association of
prokaryotes within another type of cell (primitive eukaryote).

• The eukaryotic cell is chimeric

– Eukaryotes have similar lipids and energy metabolisms to Bacteria.
– Eukaryotes have transcription and translational machinery most similar to Archaea.
– Phylogenetically closer to Archaea.

Question 17

The 2 hypothesis to explain the formation of eukaryotic cell

Answer 17

1. Eukaryotes began as a nucleus-bearing lineage that later acquired mitochondria
   and chloroplasts by endosymbiosis
2. Eukaryotic cells arose from intracellular association between a H2-producing
   bacterium (the symbiont), which gave rise to mitochondria, and an H2-consuming archaeal host. The archaeal host later developed a nucleus.

Question 18

What are Streptomyces?

Answer 18

Filamentous actinobacteria
• Hyphal growth (filament of
cytoplasm usually not separated by cross-walls)
• Produce dessication resistant
spores at the tip of an elevated
structure called sprorophore.

Question 19

What is Bdellovibrio?

Answer 19

Predatory bacteria
• Infect other bacterial cells.
• Acquire nutrients from host cells.
• Does not grow on agar plates.
• Gram-positive bacteria are not infected.

Question 20

What are Caulobacter?

Answer 20

Stalked Bacteria
• Found in aquatic environment.
• Unique cell cycle that
includes cell differentiation: sedentary stalked mother cell and a motile flagellated daughter cell.
• The tip of the stalk secrete
the stickiest substance
known.

Question 21

What is Chlamydia ?

Answer 21

Obligate intracellular bacteria
• Grow only inside host cells.
• Elementary bodies: infectious, release from host cells.
• Reticulate bodies: intracellular, active growth.
• Chlamydia trachoma5s, Chlamydia pneumoniae.

Question 22

What are the 5 archae famiy?

Answer 22

Euryarchaeota, Nanoarchaeota, Koraarchaeota, Crenarchaeota, thauarchaeota

Question 23

The polyphasic approach to taxonomy uses these methods

Answer 23

Ø Phylogenetic analysis (16S rRNA, MLST)

Ø Phenotypic analysis (motility, capsule, virulence, etc.)

Ø Genotypic analysis (presence/absence of specific genes, etc.)

Question 24

What is Multilocus sequence typing (MLST)?

Answer 24

• Method in which several different “housekeeping genes” from a species are sequenced and aligned to the respective sequences of other individuals of the same species.
• Has sufficient resolving power to distinguish between very closely related strains.

Question 25

What is identification?

Answer 25

Identification of an unknown microorganism will depend on the comparison of its
properties with those of organisms that have already been classified and name
(Type strains).
– Morphology
– Biochemical proper>es
– 16S rRNA sequencing.
– MLST

• Dichotomous key (morphology and phenotype)
• Serotyping

Question 26

What is serotyping?

Answer 26

• Based on the binding of specific antibody to surface structure:
– LPS: O serotypes (E. coli O157:H7)
– Capsule: K serotypes (Klebsiella pneumoniae K1, higher virulence)
– Flagella: H serotypes (E. coli O157:H7)

• Antibodies: molecules of the immune system that recognize and bind to molecule on the surface of a microorganism or to secreted proteins.
• Positive reaction: agglutination.