Download Life and transport in soil inner spaces

Life and transport in soil inner spaces:
Life and transport in soil inner spaces: The hidden frontier
Dani Or
Institute of Terrestrial Ecosystems (ITES)
Department of Environmental Sciences (D‐UWIS)
Swiss Federal Institute of Technology Zurich (ETHZ)
f
gy
(
)
Outline •
Soil ecological functions – Earth’s life support system
•
Repository of largest biodiversity – scope •
Bacterial life in soil –
ac e a e so factors promoting diversity ac o s p o o g d e s y
•
Aquatic habitats, complex soil pores, diffusion, motility
•
Biophysical modeling ‐ bacterial coexistence at microscale
Biophysical modeling ‐
bacterial coexistence at microscale
•
Preliminary experiments with real bacteria: coexistence and motility under limited hydration and diffusion y
y
•
Lessons and conclusions
•
STEP forward
STEP forward
Water Film
Pendular
Water
r(μ)
R
H
α
Soil ecological functions
• Soil is the most biologically active compartment of the biosphere hosting the largest pool of
of the biosphere hosting the largest pool of biodiversity • Soil is a giant recycling system, it provides most of our needs for food, feed, fiber and wood, and supports most stocks of global biomass • Earth
Earth life support system ‐
life support system ‐ soil functions as soil functions as
Earths' life support body, a thin film of life covering much of terrestrial surfaces
• A natural body ‐ soil is a functioning complex natural body with unique characteristics that cannot be deduced from a collection of its constituents or individual processes
(NASA)
Soil ‐ provisioning and regulating services
• Provides anchoring and growth media for higher plants (>95% global biomass)
• Serves as water reservoir and functions as a water purification system
as a water purification system
• It is nature’s recycling system –
biogeochemical cycles (C, N)
• Provides habitats to the largest number of species in the biosphere
• U
Used as building material and provides d b ildi
t i l d
id
foundation for engineered systems
The economic value of soil services is estimated at $100 Trillion (1012) per year exceeding annual global GNP f $70 T illi (C
GNP of $70 Trillion (Costanza
et al. 1997; Young 2006)
l 1997 Y
2006)
Soil ‐ an environmental interface
• Soil forms interfaces between the lithosphere, atmosphere, hydrosphere, and the biosphere
yd osp e e, a d e b osp e e
• Soil interfacial functions span many scales – molecular to continental
• Thin soil skin affects/regulates large scale atmospheric processes
p
p
• Soil is characterized as a medium with large interfacial area per volume (surface area >100 m2/g)
(Brady and Weil 2001)
Soil and early civilizations • The importance of soil to mankind is reflected
in the language; in Hebrew Adama=soil the origin of Adam’s name (and creation) and Human
f d ’
( d
) d
h
has its roots in soil Humus (organic matter) • Early
Early civilizations in Mesopotamia, Egypt, and Indus
civilizations in Mesopotamia Egypt and Indus
Valley flourished (~2300 BC) on fertile and irrigated lands
• Evidence suggests that soil degradation primarily by salinization due to excessive irrigation may have caused their demise (loss of land >800,000 km2 in Indus Valley)
Soil – repository of unparalleled biodiversity
• Soil is the richest compartment of life hosting unparalleled microbial diversity at all scales
• Soil bacterial density is 200,000 times higher than found in oceans (Whitman et al., 1998) • Two
Two million species in all oceans and four million million species in all oceans and four million
species in one ton of soil! (Curtis et al., 2002)
www.eyeofscience.com
• Thousands to millions of genotypes/OTU in one gram of soil (Torsvik 1990; Schloss and Handelsman, 2006); uniform (no dominance) diversity pattern • Soil fungal, archaeal, and viral communities are as diverse as soil bacteria
• A handful of fertile soil contains billions of microorganisms !
?
=
Diversity and microbial life in soil
• Soil
Soil spatial and temporal heterogeneity and spatial and temporal heterogeneity and
numerous interfaces form multitude of unique niches essential for promoting high biodiversity level – exact mechanisms remain unclear
level exact mechanisms remain unclear
Hans Joerg Vogel – UFZ (2009)
• Study focuses on biophysical interactions (heterogeneity, aquatic habitats, diffusion); however, other factors such as chemical and
biological are equally critical
Young et al. (2008)
• Bacteria are not passive – they are motile, form colonies and engineer their immediate
colonies, and engineer their immediate environment by producing EPS Vandevivere and Baveye (1992)
Objectives Primary objective: to quantify the role of biophysical factors (hydration and pore space heterogeneity) in promoting and
(hydration and pore space heterogeneity) in promoting and sustaining the enormous biodiversity found in soils r(μ)
To quantify effects soil hydration status (partial saturation) on substrate diffusion and bacterial motility
To present a modeling framework for quantifying effects of partial hydration on bacterial growth & coexistence on unsaturated surfaces
unsaturated surfaces
To present experimental observations for the roles of hydration heterogeneity and diffusion on bacterial
hydration, heterogeneity, and diffusion on bacterial colony growth rates, coexistence, and motion on surfaces
H
R
α
Fragmentation of aquatic habitats
• Water retained in unsaturated soils is held b
by capillarity and adsorptive forces in ll
d d
f
“islands” loosely connected by thin liquid films coating the solid surfaces
• The resulting fragmentation of aquatic habitats limit substrate diffusion and restrict microbial motility colony expansion • Water‐induced spatial isolation with heterogeneous nutrient/flux pathways is critical to promoting and sustaining the high degree of soil microbial diversity found at very small scales Life in complex pores bounded by liquid films
• Soil pore spaces formed by aggregation of minerals are typically angular not cylindrical
• Angularity allows dual‐occupancy of water and air hence aquatic habitats are found in “corners” behind air‐water
behind air
water interfaces
interfaces
• Aquatic habitats in unsaturated soil are often too small to support full immersion or free swimming of bacterial cells irrespective of pore size
fb
i l ll i
i
f
i
• Aquatic network structure and connectivity in complex pore spaces is highly dynamic and fragile p p
p
g y y
g
Hans Joerg Vogel – UFZ (2009)
Bacteria are not passive – formation of colonies
• An
An individual bacterium cannot modify its individual bacterium cannot modify its
environment – a crucial strategy is to form bacterial communities by pooling resources to better cope with environmental changes
• Colonies are highly organized structures attached to solid surfaces anchored and coated by Extracellular Polymeric Substances (EPS) • Soil bacteria are mostly stationary and rely on diffusion processes (saturated/ convective episodes are rare and motility is limited)
episodes are rare, and motility is limited)
wet (open)
dry (dense)
Roberson & Firestone (1992)
Bacteria are not passive – motility
• Flagellar motility and other forms of bacterial motion are necessary for
bacterial motion are necessary for arrival to and colonization of new surfaces
• Motility
Motility is also critical for local positioning within is also critical for local positioning within
heterogeneous diffusion fields on soil surfaces (scales of 10‐3 m)
www.realcaos.com
• Most previous studies focus on microbial life in aqueous solutions or saturated porous media • B
Bacterial motion and colony expansion in t i l
ti
d l
i i
unsaturated soil is limited by pore space, film thickness and aquatic connectivity Turner & Berg 2000
Rough surfaces: 2‐D observable analogues for real soil • Direct observations are hindered by soil opacity and modeling at microbial scale is too complex in real pore spaces • Rough
Rough surfaces are used for modeling and surfaces are used for modeling and
observation of bacterial life in analogue unsaturated soil habitats
• Key processes such as heterogeneity and hydration effects on diffusion and bacterial activity remain analogous
• For example, diffusional field on rough soil surfaces is determined by roughness geometry and matric potential
geometry and matric
Idealized surface roughness network
Hydration effects on diffusion and connectivity
Effective diffusion coefficient
Connected cluster distribution
Width (mm
m)
2.5E-02
Simulation L to R
Simulation U to D
PMQ
2.0E-02
wet
12
8
4
0
16 0
‐1.2 kPa
4
1.5E-02
Width (mm
m)
Efffective diffussion (mm 2/h
hr)
16
1.0E-02
5.0E-03
8 12 16
Length (mm)
dry
12
8
4
‐3.5 kPa
0.0E+00
0
0
wett
-1
-2
-3
-4
Matric potential (kPa)
-5
d
dry
0
4
8 12 16
Length (mm)
Modeling coexistence on unsaturated surfaces
• Simulations of two bacterial species growing on partially‐hydrated surfaces competing for nutrients
• Hybrid model ‐ nutrient diffusion field modeled as continuum (diffusion‐reaction model); bacteria as individual random walkers that metabolize, move about, gather nutrients, grow and divide • Typically, two species with different physiological traits inoculated on surfaces with similar nutrient and
traits inoculated on surfaces with similar nutrient and boundary conditions
• Focus on effects of heterogeneity, hydration, & motility
kn
 b
2
 t  Db  b  K  n b

S

 n  D  2 n   kn b
n
 t
KS  n
Coexistence of two competing species: Heterogeneity
Homogeneous “wet” surface
Heterogeneous “wet” surface
Coexistence of two competing species: Hydration Heterogeneous “wet” surface
Heterogeneous “dry” surface
Diffusion limitations promote coexistence
High Diffusivity
Low Diffusivity
PP. putida
tid KT2240 gfp
f
P. fluorescens F113 DsRed
Two strains of Pseudomonas with dissimilar growth rates on benzoate
agar layer
l
devoid of
substrate
perforated
Teflon
membrane
agar +
substrate
Dechesne, Or and Smets (2008, FEMS)
Observing bacteria on unsaturated surfaces
Epifluorescence
microscope
Dechesne et al., (2008, AEM)
Ceramic surface f
‐15 cm
15 cm
Solution reservoir
• A simple experimental setup for controling
p
p
p
g matric p
potential of a (sterile) ceramic surface enabling direct microscopic observations of bacterial expansion rates and coexistence
Hydration and microbial coexistence
‐0.5 kPa
(wet)
‐3.5 kPa
3 5 kP
(”dry”)
Low inoculation density
High inoculation density
Dechesne et al., (2008, AEM)
Hydration affects colony expansion rates
50 
50 m
t = 12 h
Dechesne et al., (2008, AEM)
t = 4 h
Colony expansion rates
‐0.5 kPa = 1030 ± 373 µm h‐1
‐1.2 kPa = 195 ± 62 µm h‐1
‐3.6 kPa = 17 ± 1 µm h‐1
• Matric potential controls colony expansion rates on porous surfaces
• Expansion rate was 60 times faster at ‐0.5 kPa than for dryer ‐3.6 kPa
Hydration and colony expansion rates
Dechesne et al. (2008)
• Experiments verified that flagellar
motility supports faster colony expansion rates of wild type vs. non‐
flagellated mutant (∆Flim) under age a ed u a (
) u de
different matric potential values
• Diffusion was not limiting
• Flagellation becomes insignificant when surface matric potential drops below –2 kPa (still wet!) • Limitations to flagelllated expansion are consistent with reduction in
are consistent with reduction in effective water film thickness <0.1
Colonizaation rate ( 
m/h )
1200
WT
Delta Flim
1000
800
600
400
200
0
-0.5
-1
-1.5
-2
-2.5
Matric potential (kPa)
-3
-3.5
‐ 3 kPa
h<10‐6 m
Or and Tuller (2000)
Or and Tuller (2000)
Bacterial motility on unsaturated surfaces
• As water film becomes thinner, cell‐
wall interactions (F) precede the onset of a large capillary pinning force FC (film=cell) with dramatic reduction in cell velocity as:
V  V0
FM
FC 
 F  FC 
FM
20
Cell vvelocity (m
m/s)
• Maximal velocity in solution V0 ~18 µm/s is propelled by certain force needed to overcome viscous drag, FM [Berg, 2003]
150
o
120o
15
10
5
0
0.1
1
10
- Matric potential (kPa)
R
2 2

1

1
1)]2 ( R12 [
1)]2  1 )
(
(
R1 [
P sin( / 2)
P sin( / 2)
2
R1
100
Modeling hydration effects on motility
• Comparison of measured and simulated microbial cell and colony expansion rates as functions of i
f
i
f
hydration state (matric potential) are in agreement highlighting the dominant role of s rface etness
dominant role of surface wetness on motility and expansion rates
colony
individual
Limited motility enhances coexistence?
“When mobility exceeds a certain value, biodiversity is jeopardized and lost. In contrast, below this critical threshold all subpopulations dl
I
b l
hi i i l h h ld ll b
l i
coexist…” Reichenbach et al. [2007]
C.I . 
l Mot
l HT
Summary – biophysics of the hidden frontier
• Soil provides and regulates services and functions critical for life on earth
• The unparalleled soil biodiversity and life density are attributed to rich heterogeneity and interfaces among physical, chemical & bio environments
• Aquatic habitats in unsaturated soils are fragmented and loosely connected, confine bacterial life and induce resource flux heterogeneity g
y
• Simulations and experiments illustrate the roles of heterogeneity, aquatic fragmentation, motility and diffusion on bacterial growth and coexistence
• Modeling coexistence of two “virtual” species on idealized version of soil complexity reflect on the enormity of the challenge with thousands of
enormity of the challenge with thousands of species coexisting in a cm sized soil aggregate supporting numerous biogeochemical interactions in complex pore spaces – hence, as we embark on in complex pore spaces –
hence as we embark on
exploration of outer space, the “final frontier”, an inner and equally fascinating frontier is hidden just beneath our feet awaiting to be explored
just beneath our feet awaiting to be explored Soil and environmental physics – Grand challenges
• Protection of soil as a nonrenewable natural resource
• Soil processes linked to climate change • Food security and soil health and functioning
• Soils and “green water” – soil and water management ________________________________________________________
 Study of soil as a natural body not just an inert porous medium
 Injecting more rigor and basic science into study of soil functions
I j ti
i
db i i
i t t d f il f ti
 Interdisciplinarity is not optional – essential for solving complex problems our grand challenge is to understand how species abundance and distribution and coupled hydrobiogeochemical processes in soil, the most dynamic portion of the critical zone, control ecosystem services y
p
f
,
y
at the field and landscape scales [Soil Sci. Soc. Am ‐ September 2009]
Acknowledgments
• The financial support of Swiss National Science Foundation (200021‐
113442) is gratefully acknowledged • The productive collaboration with Barth Smets and Arnaud Dechesne (DTU, Denmark) is greatly appreciated; simulation studies are results of Gang Wang (PhD ‐ ETHZ) hard work and innovation
Gang Wang (PhD hard work and innovation
• Special thanks to all Soil and Terrestrial Environmental Physics (STEP) group members for their dedication and support, and for creating an exciting research and learning environment
Ongoing research:
Soil and Terrestrial Environmental Physics (STEP)
l d
l
l h
(
)
Colony expansion: edge morphology
50 m
t = 12 h
Colony edge morphology during expansion on a rough surface under ‐3.6 kPa tension
t = 4 h
50 m
Note expansion fronts are initially f
ll
diffuse and tend to follow topography/ hydration patterns (seen at larger scale)
Surface colonization from a single cell (‐1.2 kPa)
17 h
37 h
77 h
77 h