Transcript Kein Folientitel - ULR CoNISMa di Milano

University of Essex
BIODEEP-WP3
Analysis of species diversity, community
structures and phylogeny of microorganisms
and meiofauna in the Mediterranean deep-sea
hypersaline anoxic basins (DHAB)
Andrea Sass , Terry McGenity
University of Essex
Methods:
Total DNA
 Cell preservation and lysis
 DNA recovery and cleaning
Amplification of 16S rRNA gene
 Amplification of 16S rRNA gene
with eubacterial and archaebacterial
primers, labelled with fluorescent dyes
 Digestion with restriction enzymes
Genes from different
microorganisms
 Separation of DNA fragments
 Detection of label
 Community structure profile /
fingerprint
Digestion with
restriction enzyme
 Alignment of fragments
 Cluster analysis
 Find relation between environments
Gene fragments
University of Essex
Samples included in last report:
Interface brine and brine body from l’Atalante, Urania and
Bannock basins
Oxic water from different locations and depths
Samples not included:
Discovery brine and interface: DNA extracted but no
amplification possible
Sediments: no DNA could be extracted
University of Essex
Urania basin brine
Bannock basin interface
l‘Atalante basin interface
Bannock basin brine
l‘Atalante basin brine
Urania basin interface
oxic water near Discovery, 3500 m depth
oxic water near Bannock, 3000 m depth
oxic water near Discovery, 3300 m depth
oxic water near Discovery, 2500 m depth
Euclidean distance
Clustering of t-RFLP fingerprints, data from
restriction digestion with Alu I and Cfo I combined
University of Essex
Observations:
 Profiles
of brines showed unique peaks
not found in oxic water
 l‘Atalante
 Samples
and Bannock basin brine similar
from oxic water similar
 Similarity
of interface samples to each
other and oxic or brine water not consistent
University of Essex
Conclusions:
 The basin brines contain unique microbial communities
 The differences in community structure profiles
of the brines possibly reflect the difference in their
chemical composition
 A microbial community unique to the
interfaces may exist
University of Essex
approaches from June 2002:
new samples from
 All
brines and sediments
 Different
locations within the Urania basin, from different depth within
the brine
 Differentiated
depths within the Bannock and Urania basin interface all
sediments
 Amplification

with archaebacterial primers
Comparison of t-RFLP patterns of sequences from isolates and clones
with the patterns from the total community
University of Essex
Urania brines
Urania east
brine 1, 2002
Urania east
brine 2, 2002
Urania west
brine 1, 2002
Urania east
brine 1, 2001
t-RFLP fingerprints obtained after digestion with Alu I
University of Essex
Bannock brine
2001
2002
l‘Atalante brine

2001
2002
t-RFLP fingerprints obtained after digestion with Alu I
University of Essex
Bannock interface
Niskin layer 1-2


Niskin layer 1-10


8 layers
salinities 8.7-10.8%
Niskin layer 5-5
1 layer
salinity 12.7%
Niskin layer 5-8
3 layers
salinities 13.8-15.9%
Niskin layer 10-5
1 layer
salinity 21.5%


5 layers
salinities 3.8-7.6%
Niskin layer 12-5 1 layer
salinity 25%
t-RFLP fingerprints obtained after digestion with Alu I
University of Essex
Upper Bannock interface
Niskin layer 1-2
salinity 3.7%
oxic water near Bannock
basin, 3000 m depth
Lower Bannock interface
Niskin layer 12-5
salinity 25%
Bannock brine
2001
t-RFLP fingerprints obtained after digestion with Alu I
University of Essex
Niskin layer 1-2
Niskin layer 1-10
Niskin layer 5-5
Niskin layer 5-8
Niskin layer 10-5
Niskin layer 12-5
Bannock interface 2001
Bannock interface
2002
University of Essex
Sediment traps from Bannock basin
12 months
6 months
2 weeks
t-RFLP fingerprints obtained after digestion with Alu I
University of Essex
Bannock interface
Layer 1-2
salinity 3.8 %
Layer 1-10
Sediment traps
12 months
salinity 11.3 %
Layer 5-5
6 months
salinity 12.7 %
Layer 5-8
salinity 15.4 %
Layer 10-5
salinity 21.5 %
Layer 12-5
salinity 25 %
2 weeks
University of Essex
Summary of preliminary results:
 Bannock and Urania brines from different years very similar
 Brines from different locations and depth of the Urania basin
very similar
 Little changes in l‘Atalante brine
 Changes in the profiles of the Bannock interface with rising salinity
 Fingerprints from sediment trap material show most similarity to
certain samples from within the Bannock interface
 No correspondence yet found between profiles from isolates and
environmental DNA from Bannock interface
(only major peaks considered)
Conclusions:
 A community inherent to Bannock basin interface
exists
 Uniform bacterial communities in Urania brines
 Relatively stable bacterial communities in brines
University of Essex
Future work:

Closer examination of Urania interface

Profiles from more sediment trap samples
 More attempts to obtain profiles from sediments and
Discovery brines
 Amplification with archaebacterial primers