Acknowledgements: We thank the captain and crew of RV Polarstern expedition PS85 for their excellent support in the field. This study was funded by the European Research Council Advanced Investigator grant no. 294757 to Antje Boetius and the Alfred-Wegener-Institut grant no.
AWI_PS85_07.
Diversity of hydrolytic enzymes among Arctic deep-sea sediment bacteria
Josephine Z. Rapp1,2, Christina Bienhold1,2, Halina E. Tegetmeyer2,3, Claudia Pala2, Pierre Offre2,4 & Antje Boetius1,2,5
5500 m 3500 m 2500 m 1200 m
GH1 GH31 GH32 GH38 GH39 GH43 GH47 GH48 GH57 GH59 GH63 GH76 GH108 GH127GH65GH30GH28GH26GH20GH18GH16GH15GH13GH10GH9GH5GH4GH3GH2
lowest gene count per GH highest gene count per GH
European Research Council
Established by the European Commission
0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6
EGIEGIIEGIIIEGIVHGIVHGIIIHGIIHGI
0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6
EG_IEG_IIEG_IIIEG_IVHG_IXHG_VIHG_VHG_IVHG_IIIHG_IIHG_I orgC [%]
0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6
EG_IEG_IIEG_IIIEG_IVHG_IXHG_VIHG_VHG_IVHG_IIIHG_IIHG_I orgC [%] 0 5 10 15 20 25 30
EGIEGIIEGIIIEGIVHGIXHGVIHGVHGIVHGIIIHGIIHGI Phaeo [µg/ml]Chl a [µg/ml]
0 5 10 15 20 25 30
EGIEGIIEGIIIEGIVHGIXHGVIHGVHGIVHGIIIHGIIHGI Phaeo[µg/ml]Chl a [µg/ml] 0.00E+00 5.00E+08 1.00E+09 1.50E+09 2.00E+09 2.50E+09 3.00E+09 3.50E+09
HGIXHGIVHGVHGVIHGIIIHGIIHGI 0.00E+00 5.00E+08 1.00E+09 1.50E+09 2.00E+09 2.50E+09 3.00E+09 3.50E+09
HGIXHGIVHGVHGVIHGIIIHGIIHGI orgC [%]
0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6
%
0 5 10 15 20 25 30
µg/ml
HGI 1200 m
water depth
0 1*109 2*109 3*109
cells/ml sediment
HGIX 5500 m
Gammaproteobacteria Alphaproteobacteria Cytophagia
Gemmatimonadetes Flavobacteriia
SAR202 clade Acidimicrobiia
Betaproteobacteria JTB23
others
Deltaproteobacteria
others
unclassified Xanthomonadales (GP) unclassified Kl89A clade (GP)
unclassified Rhodospirillaceae (AP) unclassified Flammeovirgaceae (C) Marinicella (GP)
unclassified OM1 clade (A) unclassified SAR202 clade Pseudospirillum (GP)
unclassified BD2.11 terrestrial group (G) unclassified Halieaceae (GP)
unclassified BD7.8 marine group (GP)
unclassified JTB255 marine benthic group (GP) unclassified Sh765B.TzT.29 (DP)
100
80
60
40
20
0
DNA cDNA HGI X 5500 m
DNA cDNA HGVI 3500 m
DNA cDNA HGV 3000 m
DNA cDNA HGI V 2500 m
DNA cDNA HGI I I 2000 m
DNA cDNA HGI I 1500 m
DNA cDNA HGI 1200 m
21044 72 236
14508 63 208
21111 81 316
99297 89 362
27406 86 329
16578 80 281
32706 86 312
19035 75 288
161165 92 383
17146 77 299
42946 82 343
9079 60 235
27336 86 322
19040 77 302 nSeq
nC nG 100
80
60
40
20
0 Gammaproteobacteria
Alphaproteobacteria Cytophagia
Gemmatimonadetes Flavobacteriia
SAR202 clade Acidimicrobiia
Betaproteobacteria JTB23
others
Deltaproteobacteria
others
unclassified Xanthomonadales (GP) unclassified Kl89A clade (GP)
unclassified Rhodospirillaceae (AP) unclassified Flammeovirgaceae (C) Marinicella (GP)
unclassified OM1 clade (A) unclassified SAR202 clade Pseudospirillum (GP)
unclassified BD2.11 terrestrial group (G) unclassified Halieaceae (GP)
unclassified BD7.8 marine group (GP)
unclassified JTB255 marine benthic group (GP) unclassified Sh765B.TzT.29 (DP)
100
80
60
40
20
0
DNA cDNA HGI X 5500 m
DNA cDNA HGVI 3500 m
DNA cDNA HGV 3000 m
DNA cDNA HGI V 2500 m
DNA cDNA HGI I I 2000 m
DNA cDNA HGI I 1500 m
DNA cDNA HGI 1200 m
21044 72 236
14508 63 208
21111 81 316
99297 89 362
27406 86 329
16578 80 281
32706 86 312
19035 75 288
161165 92 383
17146 77 299
42946 82 343
9079 60 235
27336 86 322
19040 77 302 nSeq
nC nG 100
80
60
40
20
0
RNA RNA RNA RNA RNA RNA RNA
1Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, HGF-MPG Group for Deep Sea Ecology and Technology, Bremerhaven, Germany, 2Max Planck Institute for Marine Microbiology, HGF-MPG Group for Deep Sea Ecology and Technology, Bremen, Germany, 3Bielefeld University, Center for Biotechnology - CeBiTec, Bielefeld, Germany, 4Royal Netherlands Institute for Sea Research - NIOZ, Texel, Netherlands,5MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
Figure 2 - Biogenic sediment compounds and bacterial cell numbers in surface sediments in 2014. Chlorophyll A represents the contribution of fresh material, phaeopigments represent more degraded material.
Introduction
- benthic communities are dominated by bacteria of mostly unknown identity and metabolism
- most deep-sea ecosystems are sustained by exported organic material from the productive, sunlit surface ocean
- organic matter availabilty generally decreases with increasing water depth
- previous studies showed a correlation between changes in bacterial community structure and organic matter availability
Figure 1 - Samples were taken in 2014 at the Arctic Long-Term Ecological Research (LTER) site HAUSGARTEN in Fram Strait. Red dots indicate the four sites that were included in this study, located along a water depth gradient from 1200 m down to 5500 m depth. WSC:
West Spitsbergen Current; RAC: Return Atlantic Current; YB: Yermak Branch; Svalbard Branch; EGC: East Greenland Current.
Results from the different molecular appriaches were in good agreement and suggested similar community sturctures with the same dominant members.
- high turnover across the depth gradient at species level - the active community showed a higher turnover
Organic carbon Chlorophyll A + Phaeopigments Cell numbers
Main Questions
- Do we find differences between dominant and dominant active bacterial groups in Arctic deep-sea surface sediment at different water depth?
- Do communities residing at different water depths exhibit different capabilities to break down organic matter?
- Can we link specific hydrolytic enzymes to individual taxonomic groups?
Figure 3 - Dominant bacterial genera as determined by DNA and RNA tag sequencing.
- similar community composition along slope at low taxonomic resolution
- typically predominant sediment taxa, i.e. the JTB255 marine group, the Sh765B.TzT29 group or the OM1 clade, were
underrepresented in the active part of the community
- other usually low-abundant taxa, i.e. Flavobacteriia and the
Figure 4 - Community turnover along the slope at OTU level.
Displayed are Jaccard dissimilarities and OTUs > 99 reads.
Figure 5 - Heat map of protein family gene counts associated with specific glycoside hydrolases (GH). Only GHs that could be detected both in metagenomes and - transcriptomes are displayed.
Conclusion
- Benthic bacterial communities vary with water depth and exhibit a distinct enzyme machinery for the breakdown of polysaccharides depending on the type of exported material
- communities at shallower depths show a greater proportion of protein domains involved in degradation of fresh algae material - communities at deeper stations show a greater proportion of
protein domains involved in breakdown of recalcitrant material and
bacterial cell walls DNA tags
RNA tags MetaT
MetaG
CARD-FISH
Figure 6 - Community composition on class level as resolved by the different molecular approaches.
