Adaptation to Extreme Environments T NOT 37°C pH NOT 7 IAP

Transcription

Adaptation to Extreme Environments
Adaptation to Extreme Environments
HOW LIFE ADAPTS TO ENVIRONMENTAL EXTREMES
What are extreme conditions ?
How do microorganisms respond to stress situations through protection and
adapted growth behavior ?
Are extreme ecosystems model systems for early earth conditions
Kurt Hanselmann
Microbial Ecology Group,University of Zürich
1
Jöri Excursion - Geochemistry Course - University of Konstanz 28. / 29. Mai 2004
Microbial Ecology Group
University of Zürich
www.microeco.unizh.ch
2
Contents
T NOT 37°C
pH NOT 7
IAP NOT equivalent to 150 mM NaCl
pO2 NOT 0.2 atm
Energy source NOT organic molecules
Oxidant NOT O2
Life styles made for extremes
Adaptation to low nutrient conditions
Biological selection - adaptation hypothesis
Evolutionary microbial ecology
Extreme environments and exobiology
Training for astrobiology
What‘s „extreme“ ?
Environmental determinants
What is life
3
4
Range of conditions that sustain and limit life processes
Energy: ∆Gr < 0, exergonic,
High water activity habitats
Heat budget, Temperature
Radiation exposure
pmf, ∆ψ
Mass:
Nutrients:C,H,O,N,P,S, etc.
Oxidants / Reductants: Eh, pe
Water Potential
Physical state of H2O
Stability of H2O
Pressure
Ion acitivities: pH,
Functional stability
of bio-molecules:
Nucleic acids
Proteins
Lipids
buffering, IAP
Saturation IAP/Ksol
5
6
Low water potential habitats: high salt concentrations
Low water activity habitats: endolithics in desert rocks
Atacama desert; dryest place on earth
Desert varnish
Oligonucleotide and EPS
staining in situ
7
Syto 40, Lectin, Dolomite
rock. Coutesy of Th. Horath
Jöri Excursion - Geochemistry Course -
University of Konstanz 28. / 29. Mai 2004
8
High temperature habitats: hydrothermal springs
High temperature high pressure habitats:
deep sea hydrothermal vents
T ≈ 350oC, pH = 4-5
9
Photo taken from Alvin
10
Low temperature habitats: Cryoconite holes
Hydrothermal Vent Model of early Evolution on Earth
Organic synthesis took place in hydrothermal vents at midocean spreading ridges
Liquid-solid interfaces available
Strong free energy gradients
“Pyrite-pulled” reactions (Wächtershauser)
11
12
Low-temperature habitats: snow and ice
experimental ecosystems
13
Bacterial diversity in snow
14
Snow cover ecology
Survival and living in ice and snow
Physical characteristics of snow
Temporary transition layer between soil and atmosphere
Cold-extreme habitats are common:
Polar regions account for more than 14% of the earth’s surface.
90% of the oceans are colder than 5 oC
Æ How significant is the biosphere in these environments?
Fresh snow: highly porous and with interstitial air spaces
Packed snow: less porous and with interstitial water or ice crystals
Forzen snow: ±porous and with interstitial ice crystals
Melting snow: porous and with interstitial liquid water
Life in snow and ice poses a number of challenges to organisms:
T at soil-snow interface: ± 0oC, heat flux from deeper soil layers
T at snow-air interface: can be << 0oC, heat loss from snow pack
Snow and ice are oligotrophic ecosystem characterized by extremes
of dryness (low water activity) and low temperatures.
How can microorganisms thrive under the combination of extreme
conditions near the triple point of water?
Nutrient content: adsorbed to snow flakes available only during melting period
Radiation: white snow has high reflectance, „dusty“ snow absorbs mostly long
wavelength radiation, heat melts snow
15
16
Adaptive mechanisms for low temperature habitats
Contents
What is life
Stategies for living at low temperatures
•
•
•
•
Spore formation, converting into resting, non-growing stages
Production of extracellular mucilage which induces freezing around but not
inside cells
Increased intracellular solute concentration to prevent freezing damages
Changes in the lipid and protein composition of membranes to make them more
elastic
Organisms living in the cold offer insight into new life strategies and they
might lead to the discovery of new biotech-products
17
18
The Notion of a Minimal Cell
Criteria for life
how can we decide whether a particle is alive or not ?
lipid bilayer enclosed compartment
Does it have an organization ?
containing the minimal and sufficient
number of components to be „alive“
DNA, RNA, NTPs, dNTPs, amino acids, salts
Does it metabolize ?
i.e. the ability to „extract“ mass and energy from the environment
Can it reproduce itself ?
i.e. the ability to maintain the information needed to self-replicate and transform
stored information into catalytic functions
self-maintenance
„alive“
Does it respond to environmental stimuly ?
i.e. the ability to adapt to changes in environmental conditions
reproduction
mutation
19
20
Synthesizing life
Prerequisits for microbial existence
JACK W. SZOSTAK, DAVID P. BARTEL & P. LUIGI LUISI
Nature 409, 387 - 390 (2001)
21
e.g. Growth = formation of biomass
22
Assimilation requires:
Dissimilation requires:
•
•
•
•
•
•
•
•
mass: nutrients
„template“: inoculum
energy: since ∆Gr is > 0
catalytic converters: enzymes
Different ways of "how to make a living" emerge from …….
-
23
Contents
What is life
the energy conversion mechanisms possible
the presence or absence and the kind of reductants and oxidants
the metabolic processes which are employed
the kind of material resources available for biosyntheses
antibiotic compounds present in the habitat
interactions between organism and environment
competition (symbioses) between organisms
mass: oxidizable compound
chemical oxidant
release of energy if ∆Gr is < 0
energy converter: membrane
24
Ecosystem functioning depends on
geochemical cycling
Life styles
Seven of the eight major chemical elements involved in life processes are
cycled via redox reactions
Biological mass fluxes are cyclic
Mass cycles are always coupled with energy fluxes
The functioning of energy fluxes is dictated by thermodynamic laws
Disturbances in mass and energy fluxes lead to alterations in environmental
conditions and thus to changes in the kinds of life processes
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26
Redox states of some inorganic compounds involved in
biological processes
Oxidant diversity
Atom Æ
C
H
O
N
P
S
Fe
Mn
Compound
SO42-
VI+
H2S
II-
So
S2O32-
0
V+ / I-
S4O62-
V+ / 0
NO3-
V+
NO2-
III+
NO
N2O
II+
I+
N2
0
NH4+
HPO42-
IIIV+
HPO32-
III+
H+
H2
I+
0
Fe3+
Fe2+
III+
II+
Mn4+
IV+
Mn3+
III+
Mn2+
II+
CO2
IV+
CO
II+
Organic compounds for comparison
IVCH4
27
28
HCHO
0
CH3OH
II-
Non-equilibrium thermodynamics applied to microbial
processes
Contents
What is life
aA + bB ⇔ cC + dD
c
Q =
d
[C] • [D]
a
b
[ A] • [B]
∆Gr = ∆Gr o + R • T • ln Q
o
o
o
o
= - R • T • ln K = ∑ Gf (P) - ∑ Gf (S )
Q
∆Gr = R • T • ln o
K
1
∆Gr
Q
R• T
= E1/ 2 = • (∆Gr o + R • T • lnQ) = • ln o
n• F
n• F
K
n• F
∆Gr
R = 8.31451 • 10-3 [kJ • Mol-1 • o K-1], F = 96.485309 [kJ • mol-1 • V -1]
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30
Extreme and extremely variable environmental conditions in
high-mountain aquatic habitats
Characteristics of high-mountain aquatic ecosystems
→ extreme conditions for life processes
Oligotrophy
Psychrophily
Radiation
31
ice and snow cover for more than 7 month/year
generally low water temperatures
diurnally large T-fluctuations during the snow-free season
snowfall possible every day of the year
originally minimal nutrient concentrations
generally low productivity despite high radiation
high turbidity in certain habitats due to erosion particles
32
Modes of growth in low-nutrient aquatic environments
Life strategies in low-nutrient environments
Jöri-lakes during melting of the ice
effective mechanisms to harvest nutrients
high affinity for nutrients (low uptake KS)
ability to access alternative nutrient sources (solubilization of solids, release of
surface bound or encapsulated nutrients)
High affinity for nutrients, Hydrurus sp., Jör i
store intracellular reserves temporarily
organisms convert into non-nutrient requiring resting stages
Alternative nutrient sources
Mud covered cyanobacterial mats, Tambo
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Cyanobacterial mats in flowing stream, Tambo-lakes
34
Seasonal Community Shifts of Algae in Jöri XIII
Contents
Dbr
What is life
Mrp
sF
Dbr
B
A
Mrp
Mrp
D
C
A: ice melting, B: end of ice melting, C: late summer, D: beginning of ice melting
35
Gabriela Iqbal-Nava (2003)
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TTGE patterns of prokaryotic DNA during ice-cover periods:
molecular approach to analyze diversity under changing conditions
depth (m)
Large fluctuations: annual temperature at different depths of Lake Jöri XIII
depth (m)
15 Jul 02
3 Feb 02
26 Oct 01
beginning of ice-cover period
condition D
14 May 02
4 Aug 02
24 Aug 02
13 Sep 02
27 Aug 02
end of ice-cover period
condition A
Bands (numbered) indicate most abundant bacterioplankton
Munti Yuhana (2003)
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38
Temperature profiles of Lake Jöri XIII
TTGE patterns in unstable water masses
T-profiles
o
ice-covered
0
1
2
ice-free
Temperature ( C)
3
4
5
6
7
8
9
10
depth (m)
0
depth (m)
1
2
3
D
Depth (m)
4
5
6
7
B
A
8
C
9
10
11
27-Jun-02
16-Aug-02
1-Oct-02
16-Jul-02
27-Aug-02
16-Oct-02
30-Jul-02
9-Sep-02
5-Dec-02
7-Aug-02
24-Sep-02
A - D: conditions when the samples for diversity analysis were collected
instability begins
summer, condition B
39
complete mixing
autumn, condition C
Munti Yuhana (2003)
40
Seasonal nutrient fluctuations
The most abundant bacteria present in summer
Bands, closest known-species, similarity
depth
(m)
B10: Simonsiella steedae, 88%
B9: Aquaspirillum delicatum, 97%
B7: Chlorella saccharophila chloroplast, 96%
B6: Bosea minatitlanensis, 94%
B5: Verrucomicrobiae, 95%
B4: Kinetoplastibacterium crithidii, 94%
B3: Achromobacter xylosoxidans, 96%
B1: Gemmatimonas aurantiaca, 97%
A - D: conditons when the samples für diversity analysis were collected
end of ice cover period
summer
41
Munti Yuhana (2003)
Most abundant bacteria present at beginning of ice-cover period
Most abundant bacteria present in autumn
42
autumn
early winter
depth
(m)
depth
(m)
C12: Trojanella thessalonices, 89%
D12: Aquaspirillum delicatum, 97%
C11: Aquaspirillum delicatum, 97%
D11: Aminomonas aminovorus, 94%
C10: Ultramicrobacterium, 95%
D10: Bordetella avium, 97%
C9: Chlorella saccharophila chloroplast, 96%
C8: Nostocoida limicola III, 86%
D7: Polynucleobacter necessarius, 97%
C7: Polaromonas vacuolata, 97%
D6: Rhodoferax ferrireducens, 98%
C6: Rhodoferax ferrireducens, 98%
D5: Frankia sp., 91%
C5: Sphingomonas sp., 92%
D4: Leptothrix cholodnii, 97%
C4: Polynucleobacter necessarius, 98%
D3: Sporichtya polymorpha, 92%
C3: Frankia sp., 91%
D2: Frankia sp., 97%
C2: Gluconacetobacter sacchari, 94%
summer
43
autumn
early winter
D1: Gemmatimonas aurantiaca, 90%
Munti Yuhana (2003)
C1: Gemmatimonas aurantiaca, 90%
summer
Munti Yuhana (2003)
44
autumn
early winter
Adaptation - Selection Hypothesis:
Niche Specialists vs. Niche Generalists
How niche specialists respond to different conditions
D
C
B
A
45
46
Diversity of plaktonic Archaea in Jöri Lake 13
Selection is the evolutionary driving force
Ecosystems are spaces inhabited by organisms, which can make a living within the
boundaries set by the habitat conditions
(ecosystem = habitat + organisms + living conditions)
47
48
Evolution to complexity
Evaluating ecosystem complexity
1.
2.
3.
4.
5.
6.
49
50
Thermodynamic minimum test
Nutrient availability test
Diversity test
Ancestor-descendant test (phylogeny)
Stability test
Interdependency test
Contents
the study of how environmental determinants select for phenotypes
What is life
¾ which environmental determinants induce new genotypes ? (ecological selection)
¾ which genes are regulated by environmental determinants (ecological genomics) ?
51
¾ which gene products are necessary to best cope with prevailing conditions and interactions
? (ecological proteomics)
52
Lessons taught by microbes
Genomosphere Biology
Genomosphere: the sum total of the functional and regulatory
(information processing) capacity of all living organisms
• Comparative genomics of 50+ microbial genomes
• Smallest known microbial genomes (~470 ORF) still larger than a “minimal” gene
set (~200 genes)
Longest time constant (conserved protein evolution) in the climate
system (e.g., iron-requiring proteins that date from anoxic
Archean)
• Microbes with genomes of <1 Mbp capable of complex behavior (e.g.
Mycoplasma spp.)
Will the rules of regulation and evolution derived at small scales be
applicable to large scales (the whole genomosphere)?
• From one-third to one-half of ORF in microbial genomes have no known or
putative function
• Fraction of putative regulatory genes in microbial genomes typically increases
with genome size and complexity of habitat/behavior
53
54
GEO- / EXO-BIOLOGY HIGHLIGHTS
5 Priorities in Evolutionary Ecology
and Geo(micro)biology
Origins and evolution of life
Evolution of the atmosphere, hydrosphere and biosphere
The sedimentary rock record and geobiology of critical intervals
Paleobiology and evolutionary ecology
Biogeochemistry and global elemental cycles
Geobiology of weathering
Organics-microbe interactions
Microbial metal binding and Biomineralisation
Molecular ecology and phylogenetics
Evolution in extreme environments
Astrobiology
55
Microbial paleontology
Evolution of microbial diversity
Microbial involvement in global biogeochemical cycling of elements
Primary production by photosynthesis & chemosynthesis
Complexity of ecosystem functioning
56
EARLY EVOLUTIONARY ECOLOGY
Contents
What is life
Can prevailing ecological determinants be reconstructed and "dated”
from bio-phylogeny based on the DNA-record ?
Which ecological determinants might have selected for diversity, which
ones for specificity and complexity ?
How did environmental events (chronic and catastrophic ones),
influence selection, development and disappearance of phenotypes ?
Do we have evidence of biogeochemical processes which might have
been present at one time but have disappeared since ?
57
58
Geobiology focuses on 4 main aspects
What geomicrobiology can contribute to exobiology
Dimensions of space
Define process stoichiometries and process interactions
Dimension of time
Quantification of biochemical conversion rates in natural habitats
Biogeochemical cycling mediated by organisms (e.g. sulfur cycle)
Determine stability dynamics and responses towards perturbations (homeostasis)
Interactions between organisms:
Syntrophism (metabolism, thermodynamics, community analysis, FISH)
Gene exchange
Interactions between organisms and the environment
Growth compartments, space, matrix (biofilms and layered communities and habitats)
Exploitation and modification of environmental conditions (e.g. Fe-cycling)
Create ecosystem models relevant to past geochemical processes
Speculate on evolutionary processes
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60
TIME: Precambrian divisions, conditions and events
The history of life on earth
400
800
1000
LATE PROTEROZOIC
MIDDLE
PROTEROZOIC
million years bp
1400
endosymbioses
1600
approximate origin of eukaryotic cell
1800
development of ozone shield
EARLY
PROTEROZOIC
2000
transition to oxic atmosphere
2200
2400
2600
major BIF deposits
wide range of ∂13Corganic
2500
LATE
ARCHAEAN
2800
earliest eukaryotes
Biological “archives” help …
identify metabolic pathways and
regulatory mechanisms and
annotate protein sequences
0.1%
Eukarya
Archaea
Bacteria
•
Analysis of genome and proteome databases is providing an understanding of …
how life evolved,
how life conquered extreme habitats,
how the biosphere adapts to global change
phototrophic prokaryotes and BIFs
EARLY
ARCHAEAN
oldest terrestrial rocks:Isua
origin of life
3800
chemical evolution
of biomolecules
4000
4200
4600
•
stromatolites, filamentous microbes
3400
3600
Archives are …
geological strata,
the fossil record,
the genomes of contemporary organisms
origin of oxygenic phototrophs
MIDDLE
ARCHAEAN
3200
4400
1%
•
oldest known „biogenic“ ∂34S
3000
3800
20%
10%
origin of modern eukaryotic cell
1200
1600
oldest metazoen fossils
origin of metazoans
900
% O2 in atmosphere
600
evolution of metazoans
540
HADEAN
anoxic environments
4500
61
Mars: Nirgal Vallis (Viking)
Mars: North Polar Cap (residual H2O ice)
62
Mars: MOC Images
Energy sources and redox reactions in Europa‘s ocean
Is or was there
life on Mars
North Polar Cap, (residual H2O
ice)
J.K Beatty et al.
The New Solar System, 4th ed.
Malin and Edgett (2000)
J.K Beatty et al.
The New Solar System, 4th
ed.
63
Example reactions:
β, γ
2 H2O
H⋅⋅ + ⋅ H
HO⋅⋅ + HO⋅⋅
2 H⋅⋅ + 2 HO⋅⋅
H2
H2O2
H2O2
H2O + 1/2 O2
H2 + 1/2 O2
H2O
β, γ
64
Contents
Training course in GEO- / EXO-BIOLOGY
What is life
Early Biomolecular Chemistry
Earth History
Earth Systems
Physiological Diversity of Microbes
Evolutionary Ecology
65
66
Core Programs
extraterrestrial life
detection missions and
instrumentation
Goals
systems research on
extremophiles on earth
Project work across range of astrobiology disciplines
Assure appropriate funding for core program
Bring focus areas together under interdisciplinary roofs
Maintain strong connections with non-European centers for life detection research
education,
training and outreach
67
68
Focal areas in the search for extraterrestrial life
Focal points for exobiology research on Earth
Astrophysical prerequisites for the inhabitability of planets
Effects of micro-organisms on the earth’s environment and climate
geophysical modelling
Methodologies in the search for extraterrestrial living conditions
Analysis of images and spectrograms from missions
Analysis of planetary minerals, isotope fractionation and organics in meteorites, dust and in situ
during missions: interstellar chemistry
Chemical, geological and mineral records of life processes
Origin of pre-biotic molecules, molecular asymmetry and biopolymers
Chemistry applied to pre-biology
Experimental and theoretical models of living cells
The search for common ancestral living cells
Early synthesis of biomolecules, hydrophobic compartmentalization, early biochemical
pathways
Emergence of the earth’s physiology, essentially its “metabolism”
Ecological conditions which have led to the evolution of metabolic diversity
Divergence and disappearance of ecosystems and early organisms
Surface mediated catalysis
Minerals, crystals, clays
Conditions for the emergence of life
environmental, energetic and trophic determinants, minimum requirements for a functioning
biological cell
Exploitation of biological “innovations” which have emerged during evolution
Technical and environmental applications of geo-bio-chemical processes
Evolution of ecosystem complexity
genomics and systems biology
69
Geo(micro)biology
field courses for graduate students
students and
and postdoctoral
postdoctoral scientists
scientists
Mono Lake, Tufa towers
71
70

Adaptation to Extreme Environments T NOT 37°C pH NOT 7 IAP

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