Module 2B: Species concept and taxonomic methods Flashcards
Microbial systematics combines ________,
_________, and ___________ data within a framework of standards
and guidelines for describing and identifying microorganisms in a taxonomic
framework
phenotypic, genotypic, and sequence-based phylogenetic
fundamental units of biological diversity
Species
Members of a species should be
genetically and
phenotypically cohesive,
they share distinct traits
that are unique only to the species.
genetically and
phenotypically cohesive
A species should also be ________, that is, the
strains composing the species should all share a recent
common ancestor to the exclusion of other species.
monophyletic
was developed to
facilitate taxonomy, and species justifications derived from this concept are
based largely on the expert judgment of taxonomists
phylogenetic species concept
defined
operationally as a group of strains sharing a high
degree of similarity in many traits and sharing a recent
common ancestor for their SSU rRNA genes.
Species of Bacteria and Archaea
Species characterization employs a ___________ that
considers a range of different traits in making taxonomic
judgments
polyphasic approach
Traits currently considered most important for
identifying species
- genomic similarity based on DNA
- hybridization
- comparisons of SSU rRNA sequences
The degree of DNA–DNA hybridization between the
genomes of two organisms provides a measure of
their ___________
genomic similarity
is isolated from the organisms
to be compared and then sheared and
denatured.
Genomic DNA
is prepared from
organism 1 by shearing, denaturing, and
labeling the DNA
Probe DNA
Genomic hybridization as a taxonomic tool
- Genomic DNA is isolated from the organisms
to be compared and then sheared and
denatured. Probe DNA is prepared from
organism 1 by shearing, denaturing, and
labeling the DNA - Sheared single-stranded target DNA from
each genome is immobilized on a membrane
and then hybridized with the labeled probe DNA
from organism 1. Radioactivity in the hybridized
DNA is measured. - Radioactivity in the control (organism 1 DNA
hybridizing to itself) is taken as the 100% hybridization value.
Radioactivity in the control (organism 1 DNA
hybridizing to itself) is taken as
the 100% hybridization value
A value of ____________ genomic hybridization and a difference in SSU rRNA gene sequence
of _______ between two organisms is taken as evidence that the two are distinct
species.
70% or less, 3% or more
taken as evidence that the two organisms are distinct species
Genomic hybridization: value of 70% or less
SSU rRNA gene sequence: difference of 3% or more
Pairs of microorganisms are compared on
the basis of their
16S rRNA similarities and
DNA–DNA hybridization values
There are ____________ for
defining taxonomic ranks above the level of genera.
no consensus criteria
How many species of Bacteria and Archaea exist?
- No firm estimate of the number of bacterial and archaeal
species can be given at present, in part because of uncertainty
about what defines a species in these domains. But is expected to be very large.
Analyses of environmental SSU rRNA gene sequences using the
phylogenetic species concept indicate that over ___________ can coexist in a single gram of soil
10,000
different species
contains an ever-growing collection
of these sequences and provides computational programs for
their analysis and for the construction of phylogenetic trees
The Ribosomal Database Project (RDP)
Bacterial and Archaeal sequencing
16s rRNA
Fungal sequencing
28s rRNA
How to reconstruct evolutionary relationships
- Observe
- Biological records (fossils, geology-geochemistry)
- Infer from data of current organisms (chemistry, gene sequence, protein sequence)
