1. Bolbfish
The blobfish (Psychrolutes marcidus) is a fish that inhabits the deep waters off the coasts of Australia and Tasmania. Due to the inaccessibility of its habitat, it is rarely seen by humans.
Blobfish are found at depths greater than 5000 m, which would likely make gas bladders inefficient. To remain buoyant, the flesh of the blobfish is primarily a gelatinous mass with a density slightly less than water; this allows the fish to float above the sea floor without expending energy on swimming. The relative lack of muscle is not a disadvantage as it primarily swallows edible matter that floats by in front it

2. Key Questions
What are the different biomes that are important to the deep carbon cycle?
Terrestrial
marine
What is the magnitudes, rates and kinds of microbial activity in the different biomes?
Temporal/spatial scales
What are the sources and sinks of organic carbon in deep environments (biotic, abiotic, and modified)?
What limits deep life? Coupled temp-pressure- energy- porosity/perm.

3. Terrestrial Biomes
Many are hydrogen driven systems

4. Terrestrial subsurface
SLiME - subsurface lithoautotrophic microbial ecosystems
Deep cratons
Columbia River basalts
Nealson et al. 2005

5. Marine biomes Complex sources and sinks for carbon
Pelagic environments
Light-driven and dark CO2 fixation
Carbon flux to benthos, crust etc
Deep sediments
Hydrothermal vents and subseafloor crust
New eruptions and linkages
Rock hosted including the deep subseafloor
Subduction zones

6. Subseafloor fluid flow regimes + settings
fluid transport = life
JOIDES Hydrogeology PPG Report (2001)

7. Taking the Pulse of a Plate: Hydrogeological-Biological Observatories
There are over 15,000 seamounts -hydrothermal “breathing” holes?
The oceanic crust is the largest fractured aquifer on Earth
85% of the Earths magmatic
budget is focused at mid-ocean
ridges
The margins host ~10,000
gigatons of hydrate
The subseafloor biosphere may rival that on the continents?

8. Sources and sinks of carbon

9. Size spectrum of organic matter and other “things” in the ocean
From Verdugo 2004

10. Colloids in the marine environment: the most abundant form of carbon
Colloids range in size from extremely small (5-200 nm) to large (0.4-1µm). Small colloids are more abundant and can reach 109/ml whereas the larger colloids are less abundant (~107/ml)
Most of the colloids are refractory carbohydrates
There are multiple sources for colloids
Nothing known about the the possible degradation of colloids and the role bacteria play in production and consumption

11. Depth distribution of small (5-200 nm) colloid particles-concentrations (X 109 ml-1) from Wells and Goldberg, 1994

12. From Wells and Goldberg, 1994

13. Incidence, diversity and physiology of “deep” microbial communities
Incidence and diversity
Metabolism of CO2 fixing microbes
Physiology of isolated microorganisms

14. Number and metabolic diversity of microorganisms in vent and other deep-sea environments
Samples
Number of microorganisms
Metabolic and/or phylogenetic groups
Sulfide structures
>108 per gram sulfide on outer layers; 105 per gram in interior
Outer layers have both bacteria and archaea and include metal oxidizers and methanogens; inner layers contain archaea of unknown physiologies
Diffuse-flow fluids (2°C to ~80°C)
105->109 ml-1; high numbers from Galapagos particles
Extremely high diversity of bacteria and archaea (all thermal groups)
Smoker fluids (<200°C to ~400°C)
Not detected to 107 ml-1; high numbers correlate with phase separation
Hyperthermophilic bacteria and archaea from culture and molecular analyses
Hydrothermal vent plume water (2°C in horizontal plume
~105 to >106 ml-1
H2, CH4 and Mn2+ oxidizing bacteria detected by activity measurements
Deep SW surrounding vents (2°C)
103 to <105 ml-1
Limited diversity of bacteria and archaea detected and enumerated by molecular methods

15. Number of microorganisms Metabolic and/or phylogenetic groups
Number and metabolic diversity of microorganisms in deep-sea environments - continued
Samples
Number of microorganisms
Metabolic and/or phylogenetic groups
Subseafloor crust
Numbers unknown on axis; ~105 ml-1 in old crust (>4 Ma)
Different thermal groups of bacteria and archaea detected from new eruptions; unique archaea isolated from subsurface fluids
Microbial mats
>108 bacteria per gram
High numbers of S-oxidizing bacteria including Beggiatoa spp and uncultured -Proteobacteria
Sediments
>108 bacteria per gram in the surface decreasing numbers with depth
Same as for microbial mats in surface layer with sulfate-reducing bacteria and methanogens dominating the deeper layers

16. The Primary Producers

17. Questions and Issues - I: Primary Production
What is the phylogenetic and physiological diversity of the primary producers in deep-sea environments (deep sediments, crust, diffuse flow vents, sulfides, animal symbionts, plumes, microbial mats, etc)?
What is metabolic versatility of the primary producers? (CO2 fixation)
How significant is the abiotic synthesis of organic compounds (C1 - Cn) to primary production? (coupling the oxidation of organic compounds with the reduction of FeIII and S°)
How do the primary producers effect biogeochemical cycles (Metal, S, P and N)?
What is the primary production rates in situ in different vent environments?
What is the diversity of N2 fixing microorganisms and how important is nitrogen fixation to primary production?
What are the sources and sinks for biologically utilizable phosphate?

18. Ax99-59 isolated from Axial Volcano
Strict anaerobe
Thermophilic
CO2 is carbon source
H2 as energy source
Reduces sulfur species
32 min doubling time under
optimal conditions
G+C ratio if 40%
New genus in the
Aquifacales
*Also -Proteobacteria are important primary producers
Scanning electron micrograph of Ax99-59.
Under most culturing conditions this
organism produce copious amount of exo-
polysaccharide, which may be involved in
Biofilm formation. Scale bar is 1 µm
Huber, unpublished

19. PNAS 102: , 2005
A Green-sulfur photosynthetic bacteria was isolated from a submarine hydrothermal vent smoker where the only source of light is geothermal radiation that includes wavelengths absorbed by photosynthetic pigments. This organisms is an obligate anaerobe and reduces CO2 coupled with oxidation of sulfur compounds
Photosynthetic
bacteria
Chlorosomes
Morphology and ultrastructure
of GSB1 cells. Bar, 300 nm
2HCO3- + H2S  2CH2O + SO42-

20. Experiments
Design experiments to investigate the effect of spatial gradients on microbial activity
Laying the groundwork for doing focused experimental studies (with potential industrial/societal/environmental impacts)
Better descriptions of physiology of microbes
Experiments to better understand OM processing at high temperatures and pressures versus transformations to acetate, methane, etc.
Relate microbial physiology to the carbon budget at organism to community scales.

21. Fieldwork
Some environments are readily accessible and some require longer term planning and how best to sample them)
85% of magmatic budget focused at ridge, but only 2 actual observations- need more data!
There are heterotrophs in deep subsurface environments (deep OM processing)
Organic sources are potentially metabolites of the autotrophs
Need to delineate sources of metabolites
How many spores are we missing?/or cyst-like states (survival)

22. Conclusions and Implications
Astrobiology (ice habitats and impact sites)
Origin of life and paleo issues
Metabolism vs. time
Physiology
a. Metabolism
b. Survival strategies/stress responses
c. Consortial strategies
d. Genome evolutions (HGT)
Need to better define and delineate deep life and deep habitats
Possible applications
Sequestration, biofuels, etc

23. From Martin, Baross, Kelley and Russell, Nature Microbiology Rev
From Martin, Baross, Kelley and Russell, Nature Microbiology Rev. submitted