O AK R IDGE N ATIONAL L ABORATORY U. S. D EPARTMENT OF E NERGY Deep Underground Science and Engineering Laboratory (DUSEL) DUSEL S1 VaTech Workshop Geomicrobiology,

OAK RIDGE NATIONAL LABORATORYU. S. DEPARTMENT OF ENERGY

Deep Underground Science and Engineering Laboratory (DUSEL)

DUSEL S1 VaTech Workshop

Geomicrobiology, Microbial Ecology and Molecular Evolution

Presented by:Tommy J. Phelps

Contents drawn extensively from previous workshops and EarthLab Biogeoscience

Ideas and concepts gleaned from numerous co-authors



Despite poor access or control the Bio-Geo community has successes

Old water accessed at depths 1-3 km, temperature > 55°C, pH > 9, at > 10,000 L/hr

Glimpse of ancient life and energy sources?


What have we learned? Advancements in Subsurface Microbiology

• Drilling, tracer and QA/QC methodologies developed• Extended known biosphere to 3 km• Revealed biomass, biodiversity, unusual traits & microbes• Linked microbial activity with geological interfaces• Slow rates of deep subsurface microbial activity• Indications of autotrophic ecosystems• Insights into evolution and ecological genomics• Energy does not appear to be limiting the deep subsurface• Deep subsurface biosphere not linked to the surface (?)• Deep anaerobic communities fueled by subsurface

abiotic energy sources (?)


What have we learned?•All observations are consistent with the laws of physics•Transformations mechanisms include: Thermogenic, geochemical, biological, and biogeochemical

Eh/pH DiagramSubsurface populations are:

diverse, active, unusual,

possess novel traits,

represent an exploitable resource,

and are a significant fraction

of planetary biomass


*SASFiG-9 (isolated)

Detected within a water-bearing dyke/fracture at 3.2 Km depth.

strictly anaerobic; iron-reducer

optimal growth temperature = 60 oC

virgin rock temp = ~ 45 oC

* SASFiG-1

SASFiG-2

SASFiG-3SASFiG-4

SASFiG-5

SASFiG-6

SASFiG-7SASFiG-9

SASFiG-8

*

image courtesy of Gordon Southam

What have we learned?Novel indigenous microbes and communitiesNovel and unusual deeply branched sequences may be indicative of ancestral linkages, (early life?), Novel products for biomed and biotech applications

Novel Bacterial lineages unique to the SA deep-subsurface:

South Africa Subsurface Firmicutes Groups (SASFiG)

1 m


Scientific Case for DUSEL: Continuous controlled access, Long term environmental isolation, Scales of investigation

spanning cubic microns – cubic kilometers


Fundamental scientific questions :

Limits of life in the biosphere;

Functioning of deep Earth ecosystems;

Use deep subsurface microbes or products for societal benefit

Major research questions:Limits of life with regards to depth, heat, pressure, energy?

What are the sources of carbon and energy ?

Abiogenic energy sources independent of terrestrial ecosystems?

Adaptations of subsurface microbes for extreme environments?

Rates of evolution in sequestered subsurface environments?

Microbial influences on mineral dissolution and precipitation?

Potential for exploiting phylogenetic and metabolic diversity?

Long term effects of human activities in the deep subsurface?


Drilling forDrilling forsubsurfacesubsurfacelife on Mars?life on Mars?

Major Questions of the Microbial Biology and Evolution group considering

systems biology, molecular evolution, ancient molecules, and advanced technologies How long have microbes have been separated from surface ecosystems?And can evolutionary rates be quantified?

Do they exhibit genomic signatures characteristic of small population size?

Is the mutational profile, inferred from sequence analyses, distinctive, reflecting expected differences in mutagenic processes?

Do subsurface microbes show much greater spatial structuring of populations and smaller genetic population sizes? If so, does it link to processes of genome evolution?

Are genomes reduced in size and streamlined relative to their surface counterparts?

Do the remaining genes evolve faster or more slowly than surface counterparts?

What role do phage, lateral gene transfer and other mechanisms play in evolution?

How has genome content evolved in the absence of host and higher cell densities?

Do subsurface microbes lack signaling genes, quorum sensing, and gene islands?

How have they adapted to different stress regimes since some are nonexistent (UV

and oxidative stresses,) while energy, nutrient, radiation, dehydration are continuous?

How can macromolecules (eg. nucleic acid, lipids and proteins) remain stable for millennia?


• Deep biosphere and biogeochemistry

• Limits of life and survival/tolerance/adaptation

• Evolutionary gradients, eco-genomics, and primitive life

• Fluid, energy, and organismal transport

• Impact of geological formations on life/preservation

• Test for an absence of life

• Impacts of human intervention on subsurface ecology

• Relationships to energy generation and carbon sequestration

• Study ore and vein forming/disassociation and mining processes

• Geo/bio/chemical study of a fabricated petroleum reservoir

• Carbon management in geological/hydrological repositories

• Role of faults on regional fluid (energy) migration

• Engineering, imaging, robotic, and in-situ mining sciences

• Others

What kind of experiments would we like to do?


Summary

Hundreds of subsurface biogeoscientists are poised for DUSEL (e.g. >300 co-authors of Phelps and of Onstott from > 100 institutions)

DUSEL represents an exciting opportunity for collaborative interdisciplinary examination of: deep biosphere, evolution and genomics, ecogenomics of human impacts, hydrologic and fluid cycling, deep flux of energy, water/rock interactions, etc.

DUSEL is unique: Dedicated, controlled access, isolated environment, multiple scales, many disciplines, education and outreach, and HERE!

Appropriate tools have recently been developed for sample retrieval and interrogation, evolutionary genomics, detailed 3-D geophysics, and examination of coupled Bio-Geo-Hydro-Chemo-processes

Biogeoscientists have prepared for two decades ground truthing hypotheses and procedures for this grand opportunity

We look forward to DUSEL and its collaborations

O AK R IDGE N ATIONAL L ABORATORY U. S. D EPARTMENT OF E NERGY Deep Underground Science and Engineering Laboratory (DUSEL) DUSEL S1 VaTech Workshop Geomicrobiology,

Documents

o ak r idge n ational

d epartment of e nergy

deep subsurface microbes

sa deepsubsurface

deep anaerobic communities

novel products

novel traits

communities novel