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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

Bolbfish

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.

Terrestrial Biomes

• Many are hydrogen driven systems

Columbia River basalts

Nealson et al. 2005

Terrestrial subsurface

SLiME - subsurface lithoautotrophic microbial ecosystems

Deep cratons

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

Mineraldehydration

Seismically induced flow

Tectoniccompaction

Biological communities

Thermally driven flow

Gashydrates

Diffuse flow

?

?

Density driven flow

Freshwater

Carbonate platformTopography driven flow

Subseafloor fluid flow regimes + settings fluid transport = life

JOIDES Hydrogeology PPG Report (2001)

Taking the Pulse of a Plate: Hydrogeological-Biological Observatories

The margins host ~10,000 gigatons of hydrate

85% of the Earths magmatic budget is focused at mid-ocean

ridges

There are over 15,000 seamounts -hydrothermal

“breathing” holes?

The oceanic crust is the largest fractured aquifer on Earth

The subseafloor biosphere may rival that on the continents?

Sources and sinks of carbon

Size spectrum of organic matter and other “things” in the ocean

From Verdugo 2004

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

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

From Wells and Goldberg, 1994

Incidence, diversity and physiology of “deep” microbial communities

• Incidence and diversity

• Metabolism of CO2 fixing microbes

• Physiology of isolated microorganisms

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

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

Autotrophic carbon dioxide fixation pathways of hydrothermal vent Archaea and Bacteria.

Metabolic Pathway Organism examples

Domain Comment References

Calvin-Bensen cycle Thiobacillus spp Bacteria Common free-living in vent and as symbionts; aerobic or denitrifying

Karl, 1995

Reductive acetyl-CoA pathway

Planctomyces spp Methanocaldococcus jannaschii; Lost City Methanosarcinales

Bacteria Archaea

Common in all vent environments; all strict anaerobes

See Thauer, 2007 and Hügler et al., 2003 for references

Reductive citric acid cycle -proteobacteria Pyrobaculum spp

Bacteria Archaea

Strict anaerobes or microaerophiles

Hügler et al., 2005; 2003

3-hydroxypropionate/malyl -CoA cycle

Chloroflexus spp Bacteria Detected in clone libraries from magma-hosted vents and from Lost City; microaerophilic1

Strauss and Fuchs, 1993.

3-hydroxypropionate/4-hydroxybutyrate cycle

Nitrosopumilus spp2 Archaeoglobus spp

Archaea Strict anaerobes or microaerophiles

Berg et al., 2007

Unknown pathway Ignicoccus spp Pyrodictium spp

Archaea All strict anaerobes Hügler et al., 2003; Jahn et al., 2007

The Primary Producers

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?

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

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

Huber, unpublished

PNAS 102:9306-9310, 2005

Morphology and ultrastructureof GSB1 cells. Bar, 300 nm

Chlorosomes

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

Phot

osyn

thet

ic

bact

eria

2HCO3- + H2S 2CH2O + SO4

2-

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.

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)

Conclusions and Implications• Astrobiology (ice habitats and impact sites)• Origin of life and paleo issues• Metabolism vs. time• Physiology

a. Metabolismb. Survival strategies/stress responsesc. Consortial strategiesd. Genome evolutions (HGT)

• Need to better define and delineate deep life and deep habitats

• Possible applications– Sequestration, biofuels, etc

Anaerobic and aerobic microbial metabolic reactions and potential energy yields in hydrothermal vent environments1 Metabolisms Reaction G kj mol-1 Examples in vent environments

Anaerobic Methanogenesis 4H2 + CO2 → CH4 + 2H2O

CH3CO2- + H2O → CH4 + HCO3

- 4HCOO- + H+ → 3HCO3

- + CH4

-131 -36 -106

Methanococcus spp common in magma-hosted vents; Methanosarcinales at Lost City

S° reduction S° + H2 → H2S -45 Lithotrophic and heterotrophic hyperthermophilic Archaea

Anaerobic CH4

oxidation CH4 + SO4

2- → HS- + HCO3- + H2O -21 Methanosarcina spp and Delta-

Proteobacteria – mud volcanoes, methane seeps

Sulfate reduction SO42- + H+ + 4H2 → HS- + 4H20 -170 Delta-proteobacteria

Iron Reduction 8Fe3+ + CH3CO2- + 4H2O →

2HCO3- + 8Fe2+ + 9H+

Not calculated3

Epsilon-proteobacteria, thermophilic bacteria and hyperthermophilic Crenarchaeota

Fermentation CH2O → 1/3 C2H6O + 1/3 CO2 -50 Many genera of Bacteria and Archaea

Aerobic Sulfide oxidation2 HS- + 2O2 → SO4

2- + H+ -750 Many genera of bacteria; common vent animal symbionts

Methane oxidation CH4 + 2O2 → HCO3- + H+ + H2O -750 Common in hydrothermal

systems; vent animal symbionts Hydrogen oxidation H2 + O 2 → H2O -230 Common in hydrothermal

systems; vent animal symbionts Iron oxidation Fe2+ + O 2 + H+ → Fe3+ + H 20 -65 Common in low temperature vent

fluids; rock-hosted microbial mats Manganese oxidation Mn2+ + O 2 + H2O → MnO2 + 2H+ -50 Same as for iron oxidation;

hydrothermal plumes Respiration CH2O + O2 → CO2 + H2O -500 Many genera of bacteria

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