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Unformatted text preview: Diversity and Phylogeny of Microbes
Methods for Determining the Relatedness of Organisms
Morphology worked very well to tell us how macroscopic organisms are relate to each other.
This yielded the five-kingdom view: plants, animals, fungi, protests, and monera (a.k.a. the
prokaryotes). This method did not work very well for prokaryotic organisms, as they do not
look very different from one another.
Darwin and Wallace, by closely studying such things as the morphology of finch beaks on
the Galapagos Islands, developed the theory of evolution. This theory stated that all life
forms have a common origin. How all of life was related to each other could not be
discerned from morphology. 16S rRNA
Understanding what united all life forms (DNARNAprotein) gave us the means to
analyze the relatedness of organisms. What was chosen was 16S rRNA (equivalent to the
18S rRNA of eukaryotes). This yielded the current view of the three domains of life: the
bacteria, the archea, and the eukarya.
Textbook Reading Phylogenetic Classification, pg. 489-494 What you should get out of this text:
1. Know the four criteria that are used to choose genes to construct the
universal tree of life.
a) universally distributed
b) functionally homologous
c) have regions of sequence similarity
d) have regions that differ
2. Be able to explain why each of these four criteria are critical.
3. Know that 16S rRNA is the molecule of choice for most
phylogenetic analyses. Constructing the Tree of Life…Or is it a Ring?
Phylogenetic trees based on a gene such as that for the 16S rRNA are now the standard for
understanding how all organisms are related to each other. The textbook reading provides a
explanation of how a tree is constructed.
Textbook Reading Phylogenetic Trees, pg. 494-495 What you should get out of this text:
Understand how a simple tree is constructed based on evolutionary distance.
a) align sequences 1 b) determine the fraction of the total number of bases analyzed that are
different between each pair of two organisms (i.e. evolutionary distance)
c) construct tree where the sum of the branch lengths that connect two
organisms add up to the fraction determined in b)
d) know what nodes and branches represent A Ring of Life?
With the entire genome sequence of hundreds of organisms now available, efforts are now on
going to determine the relatedness of organisms based on the whole genome sequence. This
effort may be answering some of the questions that have arisen when looking at genes other
than that for the 16S rRNA. For example, depending on the genes used, trees could show the
Eukarya as being more closely related to the Archea or the Bacteria. In general the pattern
that has emerged is that eukaryotic informational genes (genes involved in transcription,
translation and other related processes) are most closely related to archaeal genes, whereas
eukaryotic operational genes (genes involved in cellular metabolic processes such as amino
acid biosynthesis, cell envelope and lipid synthesis, and so on) are most closely related to
Dr. James Lake and Maria Rivera, here at UCLA, used whole genome comparison of 10
organisms representing the three domains of life. What they found that the best fit to the data
was not a tree, but a ring with the Eukaryotes have been formed by genome fusion of a
member of the Bacteria and a member of the Archea. For more information, I have provided
a link to the website for this paper (very optional reading). From the following article:
The ring of life provides evidence for a genome fusion origin of eukaryotes
Maria C. Rivera and James A. Lake
Nature 431, 152-155 (9 September 2004)
doi:10.1038/nature02848 2 Microbial Diversity
Discovery of Microbial Diversity
A revolution in our understanding of microbial diversity was brought about by the
knowledge that 16S rRNA could be used to reveal the relatedness of organisms. Scientist
started looking at the 16S/18S rRNA from all the known organisms. What it revealed was
that the diversity of prokaryotes was far, far, far greater than anything observed with plants
or animals (see Figure 11.16 on page 314). Morphology had not even come close to
revealing this level of diversity for prokaryotes. And this finding is not because 16S rRNA
underestimates the diversity of plants and animals. In fact, the morphological and 16S rRNA
analyses agree quite well about the relatedness of plants and animals.
It had long been known that we could not culture in the laboratory the majority of cells from
an environmental sample that could be observed under a microscope. If we could not grow
these microorganisms in the laboratory, we had no way to study them. PCR (polymerase
chain reaction) changed all this. We could ask what genes were present in the DNA of these
environmental samples. PCR allowed scientist to amplify sufficient quantities of a particular
DNA sequence that they could subject that DNA to sequence analysis. PCR amplifying 16S
rRNA genes from environmental samples revealed the diversity of organisms present. There
generally would be 100’s to 1000’s of different prokaryotic organisms in an environmental
sample. Many of these organisms were from groups that had never been studied in the
laboratory before. These types of analyses have increased our depth of appreciation of the
diversity of microbial life.
Textbook Reading Sequencing 16S rDNA, pg. 495 What you should get out of this text:
Understand the general mechanism by which you can determine the diversity of
organism present in a microbial sample.
a) isolate DNA from an environmental sample
b) PCR amplify 16S rRNA gene using primers that are general for all 16S
rRNA genes or more specific primers.
c) separate the individual pieces amplified pieces of DNA (by cloning or other
d) sequence and then generate a tree 3 Bioprospecting
Bioprospecting is the “panning” of the microbial world for new products and processes. Current
estimates are that, for every one prokaryotic species we have studied in the laboratory, there are
as many as 1000 species in the environment that we have not studied. This translates to 5 to 8
million species waiting to be discovered. Now scientist can isolate DNA from environments,
break it up, clone pieces into a bacterium like Escherichia coli, and then determine whether the
E. coli clones express an interesting activity. 4 ...
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- Summer '10