?? So what is “biodiversity” ?? “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) An abstract concept ….. Different divisions: (3) genetic, species, ecosystem diversities (5) genes, populations, species, assemblages, ecosystem (hierarchical scales) A measurable entity ….. Although based on the definition of “entities”, the concept embraces “processes”. 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.
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?? So what is “biodiversity” ?? An abstract concept ….. · So what is “biodiversity” ?? “Biodiversity refers to the variety and variability among living organisms and
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?? So what is “biodiversity” ??
“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)
Although based on the definition of “entities”, the concept embraces “processes”.
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.
(n / N)2
A social construct … Biodiversity = nature conservation. Out of its neutral scientific concept, biodiversity is perceived as a value.
Species concepts
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-children-2) 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.
Finlay 2002
For microbes: everything is everywhere …Species-Area curves
(~3000 spp)
Finlay 2002
Molecular tools for the study of marine micro- diversity:
DNAPCR
Sequencing
RFLP, DGGE
Environmental Clone Librairies
FISH
Quantitative PCR
1
DNAMicroarrays
Shotgun Sequencing
Taq Polymerase
Thermophilusaquaticus.
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:
HorseradishPeroxydase
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
6) Addition of Fluorescein-Tyramide
7) Unfixed Fluorescein-Tyramide is washed
8) DNA staining with DAPI or propidium iodide
Not necessaryfor monolabelledprobes
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.
PRINCIPLE OF FLOW CYTOMETRIC ANALYSIS
Side scatter
Chl
orop
hyll
fluor
esce
nce
Each dot represents a single measured particle.
Courtesy Glen Tarran, PML
Data are displayed as dual-parameter plots of combinations of light scatterand 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.
- PICO-EUKARYOTES -
One water samples in the Pacific; - 75m35 SSU rDNA sequences
1. Moon Van der Stay et al. 2001
Results:11 already known pico-eukaryotes24 totally new phylotypes, with twonew groups of alveolate.
2. Lopez-Garcia et al. 2001
One site at the Antarctic Polar Front4 depths: 250 / 500 / 2000 / 3000m
24 complete SSU rDNA sequences
2 novel groups of Alveolatesthat 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 truncatulinoidescollected along an Indian Ocean transect.Success rate = 90%
After PCR
After RFLP (Sau 96 I)
PCR amplification : 30 centsRPLF : 20 cents
DNA extraction : 4 cents$ 0.5/reaction !!
Type I Type IIIType IV
Foissner 2002
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!!