Using secondary minerals and hydrochemistry to trace geochemical processes in the deep subsurface
V iruses in the deep subsurface
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Viruses in the deep subsurfaceBert Engelen
Phages from Rhodobacter capsulatus-affiliated strain E32 ODP Leg 201, Site 1230, sediment depth: 268 mbsf
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Viral infections appear to control microbial biomass
Viruses supply nutrients to indigenous microorganisms
Organic carbon might be shuttled via viral lysis from H2-consumers to other heterotrophic prokaryotes
Hypotheses
Where to drill?
Anywhere !
Contamination controlled, fresh, active & deep samples
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Viruses
Image: Häusler, 2007
Virus bacteriophage phage
The most abundant biological entities with 1031 viruses on our planet (Breitbart & Rohwer, 2005)
Up to ~1023 per second viral infections in the oceans (Shuttle, 2007)
Lytic cycle
Induction
Lysogeniccycle
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7 hours: no detectable VLP
19 hours: no detectable VLP (Control)
1.2 x 1010 VLP/ml (Mitomycin C)
Control Mitomycin C
10µmSybrGreen I
Induction of prophages fromRhizobium radiobacter strain P007
Control
Induced
Addition ofantibiotic
Incubation
Washing steps
time [h]0 5 10 15 20 25
0
0.5
1
1.5
2
OD
60
0
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Phages ...
… are mortality factors for prokaryotes:Contribution up to ~71% in the deep ocean (Weinbauer et al., 2003)
Up to ~90% at the surface of deep sea sediments (Danavaro et al., 2008)
Deep subsurface? Largely unknown!
Why are we interested in phages in the subsurface?
… exhibit an enormous diversity:~ 5,000 genomes per seawater sample~10,000 – 1,000,000 per sediment sample (Edwards & Rohwer, 2005)
… provide organic matter via cell lysis:The “viral shunt“ accounts for ~80% of bacterial heterotrophic production in surface sediments (Danavaro et al., 2008)
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The viral shunt
Rhizobium radiobacter, isolated from 198 mbsf
Cell
Cell
Cell
Phage
Infection of the host
Phage capsids
Cell
Production of phage particels
100 nm
Free Rhizobiophages
20 µm
DNA released after lysis of the cell
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Induction of prophages from deep subseafloor isolates
Half of the tested isolates contained inducible prophages (Engelhardt et al., 2011)
Lysogeny might be the main viral proliferation mode in the deep subsurface
Quantification of Rhizobiophages in the marine deep subsurface
Rhizobium radiobacter highly abundant (~ 5%) (Engelhardt et al., 2013)
Site specific distribution of R. radiobacter (biogeography of subpopulations)
Rhizobiophages up to 14% of the total virus numbers
Previous work on benthic phages
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Quantification of phages atvarious sampling sites
Continental margin,slope & equat. Pacific
Coastal sediments(Janssand)
Bering Sea
South Pacific
South PacificGyre
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Virus and cell abundance
Virus and cell numbers varied by 4-5 orders of magnitude among different sampling sites
Virus and cell abundance decreased with depth
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Virus-to-cell ratio
Tidal-flat sediments: about 10 (0-5 mbsf)
Continental margin: up to ~20 (>100 mbsf)
South Pacific Gyre: up to ~225 (>50 mbsf)
Tidal-flat
Continentalmargin
South PacificGyre
Increasing in oligotrophic and deep sedimentsPreservation and ongoing viral production
Constant in tidal-flat sediments Balance of viral production and decay
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50% to 80% of the total biomass
20% to 30% of the total biomass
0.2 fg per phage particle (Suttle, 2005)
14 fg per small cell (Kallmeyer et al., 2012)
Are viruses a source of organic carbon?
By exceeding a VCR of 70,total biomass consists mainly of viral-bound organic carbon
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To which extent are deep-biosphere populationscontrolled by viral infections?
What is the main viral proliferation mode in the terrestrialsubsurface?
What is the viral diversity and the host-specificbiogeography?
How relevant is the viral shunt as a factor for sustainingthe terrestrial deep biosphere?
Can heterotrophic microbial communities thrive on cellcomponents that derive from the viral lysis of autotrophs?
Questions
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Count viruses, determine down hole virus-to-cell ratio,quantify virus production
Analyse viral diversity (metaviromics if enough material available)
Determine presence and diversity of lysogenic phages by phage-induction experiments (target groups: H2-consuming acetogens, methanogens, sulfate reducers + heterotrophs)
Identify morphologic and phylogenetic diversity of induced phages
Prove viral shunt in growth experiments (cell-lysates of H2-consumers as carbon sources for indigenous heterotrophs)
Test if isolates utilize building blocks of slowly decaying viruses (DNA and proteins as reservoir of bioavailable carbon)
Identify similarities between terrestrial, limnic and marinedeep biosphere
Work loads