Download ?? So what is “biodiversity” ?? An abstract concept ….. A

?? So what is “biodiversity” ??
An abstract concept …..
“Biodiversity refers to the variety and variability among living organisms and the
ecological complexes in which they occur …” (US Congress Office of Technology
Assessment, OTA 1987)
Different divisions:
(3) genetic, species, ecosystem diversities
(5) genes, populations, species, assemblages, ecosystem
(hierarchical scales)
Although based on the definition of “entities”, the concept embraces “processes”.
A measurable entity …..
Measuring biodiversity enables to rigorously and empirically test the concepts. There is
no way to get a unique measure of biodiversity!
The most classical measure of biodiversity combine the # of species, and the evenness
or equability of their abundance.
A social construct …
Biodiversity = nature conservation. Out of its neutral scientific concept, biodiversity is
perceived as a value.
Species concepts
(n / N)2
The world is populated by organisms that form clusters of similar individuals, called species.
Speciation is the splitting of populations into different evolutionary independent units. The species
is the critical transition level between micro- and macroevolution.
There are many different ways of defining species, none of which is able to cover all known
organisms. The 2 most important are:
1) the Biological Species Concept of Dobzhansky (1937) and Mayr (1942) –a group of organisms
that can mate with each other and produce viable grand-children2) the Phylogenetic Species Concept: a monophyletic group composed of the smallest diagnosable
cluster of individual organisms within which there is a parental pattern of ancestry and descent. The
PSC brings a historical dimension that does not exist in the BSC.
For microbes: everything is everywhere …
Species-Area curves
(~3000 spp)
Finlay 2002
Finlay 2002
Molecular tools for the study of marine micro- diversity:
Shotgun
Sequencing
DNA
Microarrays
Quantitative
PCR
Sequencing
1
DNA
PCR
RFLP, DGGE
FISH
Environmental
Clone Librairies
Taq Polymerase
Thermophilus
aquaticus.
More than 2
million copies
in 20 cycles
The Sanger sequencing reaction:
Automatic DNA
sequencing using
fluorescent dyes:
Electropherogram
Denaturing Gradient Gel Electrophoresis
-fragment: around 500 bp
-GC clamp: 39-50 bp
Denaturant: Urea, Formamide,
High temperature (TGGE)
Formation of heteroduplex!!
Typical DGGE gel:
Horseradish
Peroxydase
Basic steps in FISH:
1) Collection of natural samples through filtration
2) Cells are dehydrated with EtOH
3) Cells are stored at –80 degreeC.
4) Probe hybridization
5) Washing of unhybridyzed probe
Not necessary
for monolabelled
probes
6) Addition of Fluorescein-Tyramide
7) Unfixed Fluorescein-Tyramide is washed
8) DNA staining with DAPI or propidium iodide
PRINCIPLE OF FLOW CYTOMETRIC ANALYSIS
Flow cytometers count and
analyse individual particles in a
fluid. Fast and one by one.
The analysis consist of forward
and sideward scattered light as
well as fluorescence of the cells.
The cells are funneled by a
sheath fluid in single file
through a laser beam focus at
typically 1,000 or more per
second.
The detected optical signals
from each passing particle are
digitized and listed into
correlated data.
If a sorter unit is present,
individual particles may be
sorted physically depending on
their optical signals.
Each dot represents
a single measured particle.
Courtesy Glen Tarran, PML
Chlorophyll fluorescence
Data are displayed as dual-parameter
plots of combinations of light scatter
and fluorescence depending on the
particles being analysed.
Forward light scatter is governed by
particle size and sideward scatter is
mostly sensitive for small cellular
structures.
The fluorescence, probed in several
emission bands relates to the amount of
natural cellular pigment and its
composition, and/or artificially
introduced pigment.
Applications range from simple
phytoplankton counting and sizing to
more elaborate physiological analysis,
and species recognition using artificial
neural net algorithms.
Side scatter
- PICO-EUKARYOTES 1. Moon Van der Stay et al. 2001
One water samples in the Pacific; - 75m
35 SSU rDNA sequences
2. Lopez-Garcia et al. 2001
One site at the Antarctic Polar Front
4 depths: 250 / 500 / 2000 / 3000m
24 complete SSU rDNA sequences
Results:11 already known pico-eukaryotes
24 totally new phylotypes, with two
new groups of alveolate.
2 novel groups of Alveolates
that account for 65 to 76%
of the sequences retrieved
A few new Heterokonts
ALVEOLATES
Sub-surface
Deep Sea
Globorotalia truncatulinoides
L
R
Single Cell PCR amplification (ITS rDNA) of 40 Globorotalia truncatulinoides
collected along an Indian Ocean transect.
Success rate = 90%
After PCR
After RFLP (Sau 96 I)
Type I
Type IV
DNA extraction : 4 cents
PCR amplification : 30 cents
RPLF : 20 cents
Type III
$ 0.5/reaction !!
17 bi-monthly samplings from 100m2
area of beech forest soil in Austria.
On a total of … 1000 soil ciliates!
Foissner’s estimation: at least 30 000 species of free-living
ciliates, and eventually an order of magnitude higher!!
(Corliss, 2001: 213 000 species of protists)
Foissner 2002