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The Biosphere as a Microbial

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Title: The Biosphere as a Microbial


1
The Biosphere as a Microbial Community Studying
and Modelling the Winogradsky Column
Andrew Free Institute of Evolutionary
Biology, University of Edinburgh, Edinburgh, UK.
The Darwin Trust of Edinburgh
2
Revised (Homoeostatic) Gaia Hypothesis Life
and the abiotic environment interact via
predominantly negative feedback loops, which
tend to stabilize environmental variables
within ranges compatible with life.
Gaia
The
Question
Lenton, T.M. and Wilkinson, D.M. (2003)
Developing the Gaia theory. Clim. Change 58, 1-12
3
Homoeostatic Gaia
Lucky Gaia Probable Gaia Our biosphere has
developed a set of Life-environment systems have
a tendency to predominantly negative feedbacks
by chance evolve stabilising, negative feedback
mechanisms
Probable Gaia is an interesting, informative and
plausible hypothesis
Free, A. and Barton, N.H. (2007) Gaia, evolution
and ecology. Trends Ecol. Evol., under revision
4
The Meaning and Existence of Stability
Resistance to change Resilience to
change Global stability, over
Particular species or ecosystems long (Myr)
timescales, need not be stable
system-level within conditions compatible
properties are with life.
5
Necessary Properties of a Homoeostatic Gaian
Biosphere
A global-scale biosphere that can control the
planetary environment. The evolution of
photosynthesis. Nutrient recycling
between biochemical guilds. A wide variety of
metabolic capabilities to facilitate this
recycling.
6
  • Questions arising from the consideration of
    evolutionary and ecological theory relevant to
    the Gaia question
  • Can natural selection operating in a
    spatially-heterogeneous environment lead to
    system stabilisation at the level of the
    community, ecosystem or biosphere?
  • Are evolved systems robust at all scales
    (genetic code -gt ecosystems)?
  • Do macroscopic and microscopic ecosystems show
    stability of overall properties (if not
    necessarily of species composition)?
  • Do ecosystems develop in an ordered and
    predictable manner defined by specific ecological
    goal functions?

7
  • Can such questions be tested at the global scale?
    How??
  • Modelling
  • - Traditionally done using toy models such as
    Daisyworld.
  • - More realistic models such as Flask (evolving
    microorganisms in a chemostat-like environment)
    are now available.
  • Laboratory microcosms
  • - Will be much-simplified representations of the
    biosphere
  • - Cannot hope to reproduce the evolutionary
    history of the Earth, and this is not necessarily
    relevant anyway.
  • -Necessary due to the impossibility of
    controlled experiments on the real system.

8
  • Necessary properties of an informative model
    biosphere
  • Closed system driven solely by light energy
    once initial chemical gradients are exhausted
  • Nutrient recycling of chemicals required for
    life
  • Large number of species representing the
    metabolic diversity of the whole biosphere
  • Manageable in terms of size and temporal scale
    so that replicates and the effects of outside
    perturbations can be studied

9
  • Microbes make the world go round!
  • The vast majority of diversity in
    Microbial species drive the
  • the biosphere is microbial major
    biogeochemical cycles
  • Microbes present for
    Multicellular organisms
  • 90 of Earth history for lt12 of
    Earth history
  • Microbial microcosms

10
Does a suitable microbial microcosm with the
necessary properties exist?
11
Does a suitable microbial microcosm with the
necessary properties exist? Yes the
Winogradsky column
12
Sergei Nikolaievich Winogradsky 1856 - 1953
Pioneering work on sulphur bacteria Discoverer
of the process of nitrification (first known
form of chemoautotrophy) Landmark studies on
nitrifying bacteria, nitrogen-fixing
bacteria, iron bacteria and cellulose-degrading
bacteria Developed culture methods for soil
microorganisms One of the first researchers to
work on non-medically related microorganisms,
laying the groundwork for microbial ecology
and environmental microbiology
Inventor of the Winogradsky column
13
The Winogradsky Column Pond sediment and
water mixed with an initial supply of chemicals
(cellulose, CaSO4, CaCO3) and sealed in a
tube. Illuminated for weeks or months.
Microorganisms self-organise into layers
performing complementary metabolic reactions and
recycle nutrients among themselves. Closed
system driven solely by light energy once initial
chemical gradients are exhausted Nutrient
recycling of chemicals required for life Large
number of species representing the metabolic
diversity of the whole biosphere Manageable in
terms of size and temporal scale so that
replicates and the effects of outside
perturbations can be studied
14
Predominant Organisms Carbon Cycle Sulphur
Cycle Sheathed bacteria (Fe2
oxidisers) Organic acids and Sulphur
oxidisers CO2 fixed into SO42- lt-
H2S organic matter Cyanobacteria Purple
non-sulphur bacteria Cell death Purple
sulphur bacteria Sulphur bacteria Green
sulphur bacteria S0 lt- H2S Anaerobic
decomposers Organic acids and Sulphur-reducers an
d sulphur-reducers CO2 released by S0 or SO4 -gt
H2S decomposers
O2
Air
Aerobic water
Anaerobic water
Anaerobic sediment
H2S
15
The Winogradsky column in comparison to a
stratified freshwater lake
16
  • How to make a Winogradsky column
  • a pictorial guide!

17
Step 1 Collect some pond water.
18
Step 2 Take your trowel (and mind the wildlife!)
19
Step 3 Collect plenty of sediment.
20
Everyone can have a go.
21
including students
22
Step 4 Sieve your sediment, and mix in
CaSO4, CaCO3 and cellulose.
23
Step 5 Pack the mix carefully into clear
plastic or glass tubes, then add the water on
top.
24
Step 6 Incubate for weeks or months
with illumination.
25
Winogradsky Columns After 9 Weeks Incubation
Fe-oxidising bacteria?
Purple (sulphur or non-sulphur) bacteria?
Green sulphur bacteria?
Anoxic sediment (black due to FeS)
Unsealed Tubes Sealed Tubes
26
Programme of work
27
Systematic characterisation of the Winogradsky
column system using modern methods from molecular
and environmental microbiology has never been
attempted We need to start at the beginning!
28
  • 1. Reproducibility of column development -
    macroscopic properties
  • 2. Development and reproducibility of chemical
    gradients - microelectrodes
  • 3. Reproducibility and order of ecological
    succession - compare to theory

29
  • 4. Species diversity within the layers over time
    - compare to theory
  • 16S rRNA gene sequencing
  • DGGE fingerprinting
  • 5. Which organisms are actively metabolising? -
    stable isotope probing
  • 6 CO2 6 H2O -gt C6H12O6 6 O2
  • SO42- 8 H -gt H2S 2 H2O 2OH-

30
  • 6. Effect of perturbation - e.g. temperature,
    irradiation
  • 7. The role of spatial structure? - a well-mixed
    column

31
  • 8. Can we construct an artificial Winogradsky
    column from sterilised sediment water and a
    selection of different organisms?
  • - Study evolution and diversification of the
    initial strains
  • - Test theories about the effect of order of
    ecosystem assembly on resulting system properties
  • - Test our understanding of the whole system

32
A systems perspective of the Winogradsky column
33
The Concept of Distributed Metabolic Networks
A B C
F E
D
Two-Species Partnership Byproduct
Reciprocity Syntrophy
B A

C F
D
E
B C A
D F E
Intracellular Metabolic Cycle
Distributed Metabolic Network Microbial
Consortium
34
Syntrophy by Interspecies H2 Transfer
2 CH3CH2OH 2 H2O -gt 4 H2 2 CH3COO- 2
H ?G0 19.4 kJ/reaction
4 H2 CO2 -gt CH4 2 H2O ?G0 -130.7
kJ/reaction
H2
E

Ethanol fermenter Methanogen
Coupled Syntrophic Process 2 CH3CH2OH CO2 -gt
2 CH3COO- 2H ?G0 -111.3 kJ/reaction
35
Anoxic Decomposition by a Microbial Community
Fallout of cell debris (complex polymers)
Methanogenesis
CH4 CO2
Anoxic
Sediment
Acetate-
Methanogens
Aceto- genesis
Acetogens
Methanogens
Cellulose, other polysaccharides, proteins
Methano- genesis
H2 CO2
Cellulolytic and other hydro- lytic bacteria
Hydrolysis
Acetate-
Fermentation
Propionate- Butyrate- Succinate2- Alcohols
Fermentative bacteria
Fermentation
Monomers sugars and amino acids
H2-producing, fatty- acid oxidising syntrophs
Energetically-unfavourable reactions
36
Modelling the Winogradsky column (Rosalind
Allen, School of Physics, University of
Edinburgh)
37
Group the microbial species by biochemical guild
or ecotype
Oxygenic Sulphate- Nitrifier
Anoxygenic photosynthesiser reducer
photosynthesiser
Assign a stochiometrically-correct single
reaction to each, with realistic energetics
Growth of biomass within each guild depends on
levels of relevant nutrients, uptake of those
nutrients, and presence of chemical inhibitors
(e.g. O2) Inclusion of a uniform death rate
allows recycling of nutrients from organic matter
38
Inclusion of spatial structure in the model
Uniform 2-box Multi-box
Oxic Anoxic
Easy to code but Allows separation
of Represents concentration unlikely to
work? oxic and anoxic reactions gradients well
39
Modelling the Winogradsky column will Test
our understanding of the whole system Allow
incorporation of new data from the experimental
studies as they become available Enable us to
test the likely effects of various perturbations
in silico Inform the design of perturbation
and assembly experiments
40
Acknowledgements Simon Allen (School of
Geosciences, Edinburgh) - introduction to Gaia
theory Rosalind Allen (School of Physics,
Edinburgh) - lab space, chemicals and equipment,
discussions, enthusiasm, etc., etc. -Lucas Black
- technical assistance, discussions and
wellies! Nick Barton (Institute of Evolutionary
Biology, Edinburgh) - evolutionary and ecological
guidance Jim Prosser (Aberdeen) - discussions
and assistance with techniques Tim Lenton/Hywel
Williams (Norwich) - discussions Jen Bell
(Institute of Cell Biology, Edinburgh) - THE
IDEA! Ken Murray and the Darwin Trust of
Edinburgh - Research fellowship
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