Exploring microbial communities in the dark ocean

1. Exploring microbial communities in the dark ocean Carlos M. Duarte (CSIC, Mallorca, Spain) C-MORE Symposium, UH July 11, 2008

2. Biological Oceanography: Emphasis in the top 200 m of the ocean

3. Exploring the dark Ocean: • 95 % of the Ocean volume: The largest habitat in the Biosphere. • Believed to be azoic until 19th Century. • First estimates of metabolic rates in 60’s • Grossly undersampled. • Still believed to be a compartment of the Earth System with little biological activity (Alvin lunch box story) HMS Challenger 1873-1879 “The depths of the Ocean” Murray & Hjort, 1912

4. ROV Quest, Bremen, DE ROV Isis, NOC, UK Only the 7 Nations Have the Technology to Directly Observed the Deep Ocean Nautile, D. Desbruyères, Ifremer, FR AUV ABE, C. German, WHOI, USA

5. Chemosynthetic Deep Sea Ecosystems? The Rest of Us have to use our Fantasy:

6. Microbial abundance and activity decline toward the ocean interior Arístegui, Gasol Hendl & Duarte (in prep)

7. Relationships between prokaryote community properties and Depth Arístegui, Gasol Hendl & Duarte (in prep)

8. BUT, the dark ocean’s water column is far larger… And dark ocean prokaryote biomass exceeds and is comparable to, respectively, that in the epipelagic Arístegui, Gasol Hendl & Duarte (in prep)

9. Three connected communities: A general relationship between the abundance and production of mesopelagic and bathypelagic prokaryotes and those of epipelagic prokaryotes Arístegui, Gasol Hendl & Duarte (in prep)

10. Oxygen deficiency in the deep ocean indicates significant biological activity

11. The number of estimates of pelagic respiration rate declines exponentially toward the ocean interior Aristegui et al. (2005)

12. Integrated R in the Dark ocean (> 200 m ) = 38.1 Gt C yr-1 An intermediate R maximum Exponential rate = -0. 53 0. 06 km-1 vs .-1.38 km-1 for production… Aristegui et al. (2005)

13. Repiration in the Dark Ocean K = 0.505 ± km-1 50 % of total below 800 m 10 % of total below 4,500 m Aristegui et al. (2005)

14. Respiration in the open ocean: • Total Respiration in the Open Ocean Gt C year-1 • Photic ocean (0 - 200 m) 37 - 421 • Dark ocean (200 - 1000 m) 18 - 38 • Mesozooplankton 32 • Vertebrates 0.012 • Benthic R 0.652 • TOTAL ~ 58 - 83 All based on indirect estimates (ETS): Are they reliable? The dark ocean contributes about half of the total respiration in the open ocean Requires New production (+ lateral inputs) to be ~ 20 - 40 Gt C/year 1. Duarte & Agustí (1998), Williams (1998) 2. del Giorgio & Duarte (2002)

15. Direct estimates of mesopelagic respiration (NE Subtropical Atlantic) Aristegui et al. (2006)

16. Mesopelagic respiration 600 m : 0.35 ± 0.08 µmol O2 l-1 d-1 1000 m : 0.08 ± 0.03 µmol O2 l-1 d-1 Mesopelagic R (integrated using rel. R vs. bacterial abund.): 0.22 ± 0.05 µmol O2 l-1 d-1 previous est. 0.02 µmol O2 l-1 d-1 Mesopleagic R = 90 ± 10 mmol CO2 m-2 d-1 Epipelagic R = 89-136 mmol C m-2 d-1 Aristegui et al. (2006)

17. Are previous estimates correct? R/ETS of 0.09 Based on Senescent Bacterial Cultures Christensen et al. Mar. Biol., 55, 267-276 (1980); Packard et al. Deep-Sea Res. I, 35, 371-382 (1988) Empirical mesopelagic R/ETS ratio = 0.90 R/ETS = 1.1 (range 0.6-1.7) during exponential growth phase of the cultures used to derive the R/ETS in their senescent state Christensen et al. Mar. Biol., 55, 267-276 (1980); Packard et al. Deep-Sea Res. I, 35, 371-382 (1988) Results consistent with inferences derived from mesopelagic prokaryote production and growth efficiency (decreases with depth) Aristegui et al. (2006)

18. Can Dark Ocean Respiration Be So Much Higher (x 2 to x 5) than the Epipelgic ToC Export? Two attitudes: • The community: Impossible!, We “know” this can’t be right!, (Respiration estimates are obviously wrong). • Maybe1… but this will require non-photosynthetic autotrophic production be significant in the dark ocean. 1. Says the deviant ant. Aristegui et al. (2006)

19. About 10 papers are published every year reporting new metabolic pathways present in marine prokaryotes. • e.g. anaerobic ammonia oxidizers (anammox). • Together with Euryarchaea and possibly also anammox-Planctomycetales, Crenarchaea thrive in a predominately autotrophic life mode in the mesopelagic realm. • The amount of inorganic carbon fixed in the meso- and bathypelagic ocean has been estimated to amount to be > 1 mmol C m-2 d-1 (Herndl et al., 2005), ~ 1 Pg C yr-1 • How much autotrophy may we be missing from unknown metabolic pathways (n)? • Total = Σ pathways (n) Functional genomics, transcriptomics and proteomics! n 1 Aristegui et al. (2006)

20. Nature Biotechnology (2005)

21. Blue Gold Nature Biotechnology (2005)

22. Pyrococcus furiosus The bacteria Pyrococcus furiosus, is the fastest growing known organism (1 doubling every 37 min) at 100 º C and perhaps the only organism known to use Tungsten Genetic Resources

23. Godfrey et al. 1996 Applications • Proteins isolated at high temperatures are potentially useful for biotec applications. • e.g. Tfu polimerase used in PCR, isolated from the bacteria Thermococcus fumicolans in hydrothermal vents by IFREMER scientists

24. Technology driven exploration: Toward the Petabyte Age in genomic research Arnaud-Haond and Duarte (in prep)

25. Exponential growth in reported whole-organism genome sequences Arnaud-Haond and Duarte (in prep)

26. Microbial genomes are relatively small, so whole organism genomes can be sequenced rapidly Arnaud-Haond and Duarte (in prep)

27. A frenzy of patenting of the machinery of marine organisms 150 M US $/year in patent use An amylase, extracted from deep-sea prokaryotes (Topt 105 ºC pHopt 4.5) Used to liquify corn starch for the biodiesel industry. P. Turner, G. Mamo, E. N. Karlsson,  Microbial Cell Factories. 6 (2007) Arrieta et al. (in prep)

28. Arrieta et al. (in prep)

29. A significant contribution of Prokaryotes among patented gene sequences (more modest contribution to MNP’s and no aquaculture products… Arrieta et al. (in prep)

30. The Malaspina 2010 Expedition commercial A journey to explore dark ocean pelagic biodiversity Budget: 6.5 million € + ship time (9 months) 27 Spanish institutions ~90 PI’s, 250 scientists Seaking international collaborators!

31. Take home messages The dark ocean, the largest habitat in the Biosphere, supports significant microbial populations and far more metabolic activity that we thought. The dark ocean ecosystem is not entirely dependent on epipelagic C excedents because of non-photosynthetic autotrophic processes, possiblymany yet to be discovered. The discovery of new metabolic pathways requires an impulse to genomics, transcriptomics and proteomic research. The resources and effort investment will pay off, as these genetic resources may contain the “blue gold” for biotechnology.

32. Not a homogeneous environment… POC data compilation BATS OMP (Northwest Atlantic) HOT California current Azores front Canary Basin NABE Oceanic waters Southern Ocean transition waters Arabian sea OMEX-I Ocean margin waters CORICA

33. The Deep Ocean Scattering Layer: An ecosystem still to be explored… Night Day Time Deep Scattering layer Putzeys, Hernández-Leó, & Bécognée