Sulfate reducing prokaryotes in Eastern Mediterranean
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Transcript Sulfate reducing prokaryotes in Eastern Mediterranean
Sulfate reducing prokaryotes in
the Eastern Mediterranean
A functional genomics approach
• Sulfate reduction:
– SO42- + 8H+ +8e– Electron donors
S2- + 4H2O
• Organic matter (lactate, acetate, ethanol, etc)
• H2
• CH4
– Important in anoxic marine ecosystems but
occurs in other ecosystems as well.
Sulfate reducing prokaryotes
• Dissimilatory sulfite reductase (DSR)
– Enzyme involved in sulfate reduction
– Catalysis following reaction:
– The gene encoding for enzyme contains
conservative and variable sites
– Therefore a good gene to study diversity of
sulfate reducing prokaryotes in the
environment
Deep hypersaline brines
• Eastern Mediterranean contains
hypersaline brines which are located at
the deep-sea.
• These brines are characterized by high
salinity (up to 30% salt), high pressure
(up to 350 bar) absence of oxygen and
relatively high concentrations of sulfate
and sulfide.
Deep hypersaline brines
• 16S rDNA sequence analysis revealed
many sequences related to δproteobacteria.
• Sulfate reduction rates ranged from 8 to
80 µmol H2S day-1 in the different brines.
• Conclusion:
– Sulfate reduction occurs as a metabolic
process in deep hypersaline brines
Objectives
• What is the similarity of SRP communities
between different sampling sites
• Is their similarity between DSR sequence
analysis and 16S rDNA sequence analysis.
• What is the community structure of sulfate
reducing prokaryotes (SRP)?
Mat & Meth
• Study sites:
– L’Atalante brine and interface
– Urania brine and interface
– Eastern Mediterranean deep-sea sediment three
layers
• α- and β-subunit of DSR gene amplified
• 700 bp of α-subunit were sequenced
• Amino acid alignments were created and trees
were constructed using these alignments
Diversity and Similarity
Diversity
Atalante brine
Atalante interface
Urania brine
Urania interface
Sed1
Sed2
Sed3
DSR
δ-16S
DSR
δ-16S
DSR
δ-16S
DSR
δ-16S
DSR
DSR
DSR
Sequences
100
18
100
6
100
28
100
16
22
21
10
Shannon index
1.5
2.0
0.99
1.3
0.28
0.71
1.67
1.2
1.3
2.0
1.6
Urania interface
Sed1
Sed2
Sed3
Similarity
AB DSR/16S
AI DSR/16S
UB DSR/16S
UI DSR/16S
Sed1 DSR/16S
Sed2 DSR/16S
Sed3 DSR/16S
Atalante brine
Atalante interface
Urania brine
DSR
δ-16S
DSR
δ-16S
DSR
δ-16S
DSR
δ-16S
DSR
DSR
DSR
1
1
0.26
0.00
0.00
0.22
0.00
0.05
0.00
0.00
0.00
1
1
0.00
0.00
0.00
0.03
0.00
0.00
0.00
1
1
0.00
0.31
0.00
0.00
0.00
1
1
0.00
0.00
0.00
1
0.00
0.00
1
0.00
1
Nearest relatives DSR-protein
OTU
Nearest relative
similarity
46 AB 56
Desulfohalobium retbaense
83.4%
11 AB 29
Desulfohalobium retbaense
83%
11 AB 90
Desulfobacter vibrioformis
85%
23 AB 95
uncultured deep-sea hydrothermal vent 1
77%
75 AI 36
Desulfobacter vibrioformis
86%
6 AI 18
Desulfobacter vibrioformis
86%
5 AI 60
unidentified bacterium
87%
8 AI 37
uncultured deep-sea hydrothermal vent 1
76%
94 UB 28
uncultured deep-sea hydrothermal vent 1
76%
11 UI 91
Desulfobacter vibrioformis
85%
5 UI 15
Desulfobacterium oleovorans
82%
5 UI 7
Desulfobacterium oleovorans
85%
6 UI 43
uncultured bacterium 1
84%
11 UI 14
unidentified bacterium
92%
52 UI 75
unidentified bacterium
93%
13 Sed1 01
uncultured bacterium 2
84%
7 Sed2 09
uncultured Guaymas Basin
64%
3 Sed3 01
uncultured deep-sea hydrothermal vent 1
84%
Phylogenetic tree
DSRa-protein
Phylogenetic tree
δ-16S rDNA
δ-Proteobacterial family distribution
100
90
Percentage of clones
80
70
60
Dulfohalobiaceae
Desulfobacteriaceae
50
Desulfovibrionaceae
Desulfobulbaceae
40
30
20
10
0
DSR
AB
16S
DSR
16S
AI
DSR
16S
UI
DSR
16S
UB
Origin of sulfate reduction
Desulfobotulus sapovorans
Desulfohalobium retbaense
Desulfobacula toluolica
Desulfovibrio fructosovorans
Desulfosarcina variabilis
Desulfotomaculum kuznetsovii
Archaeoglobus profundus
Archaeoglobus fulgidus
Desulfotomaculum ruminis
Thermodesulfovibrio islandicus
Percentage of clones without insertion
100
90
percentage of clones
80
70
60
50
40
30
20
10
0
AB
AI
UB
UI
sed1
sed2
sed3
Conclusions/Discussion
• All sites sampled showed diverse sulfate
reducing prokaryotic communities except
Urania brine.
• The low diversity in Urania brine has been
observed with total community structure as
well.
• Similarity of DSRa sequences between sites is
very low thus each site studied had a unique
sulfate reducing community.
• There are some differences between site
similarity of DSRa and δ-16S rDNA. Can be
related to OTU cut-off value or that not all
DSRa sequences are from δ-proteobacteria
Conclusions/Discussion
• The obtained DSR-sequences show low
similarity with GenBank sequences and
represent yet-unknown DSRa genes from
sulfate reducing prokaryotes.
• The DSRa and 16S rDNA tree topology
and family distribution were similar for
AI, UB and AB.
• This was not true for UI. UI DSRa
sequences distantly related to
Desulfotomaculum but no 16S rDNA
sequences related to that cluster.
Conclusions/Discussion
• This can be caused by
– 1. These DSRa sequences are related to the
δ-16S rDNA sequences but this cannot be
seen because tree topologies are non
congruent
– 2. 16S rDNA sequences of UI related to
unknown or candidate division clusters,
from which metabolic capacities are
unknown, are from prokaryotes with sulfate
reducing capabilities.
Conclusions/Discussion
• Allmost all DSRa sequences from deep-sea
brines and interfaces contain an insertion in αsubunit.
– This might indicate that sequences are from nonthermophilic sulfate reducing prokaryotes
• Most DSRa sequences from intermediate layer
sediment miss this insertion.
– This might indicate that sequences are thermophilic
sulfate reducing prokaryotes. This agrees with the
thermogenic history. Why these sequences only
occur at the intermediate layer is presently
unknown.