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Chapter 4 - The Terrestrial Environment
Objectives:
1. Understand the terrestrial environmental from an integrated physical,
chemical and biological perspective.
2. Define a surface soil, the vadose zone, and the saturated zone.
3. Define components of soil discussed in class such as texture, pore size
distribution, organic matter, soil structure, interaggregate and
intraaggregate pores, cation exchange, soil water potential.
4. Understand how soil water potential relates to microbial activity.
5. Understand the basics of contaminant sorption and microbial sorption.
6. Understand how microbial activity can influence the soil atmosphere.
7. Be able to describe the types, numbers, and relative activities of
microbes found in surface soil, vadose zone, and saturated zone
environments.
8. Discuss the respective competitiveness of the bacteria,
actinomycetes, and fungi in soil.
Vadose zone
Saturated zone
shallow aquifers
intermediate aquifers
deep aquifers
Scale can range from 10 to 100’s of meters
Surface soils
Surface soil (unsaturated)
X
Vadose zone (unsaturated)
Capillary fringe (nearly saturated)
Water table
Spontaneous
water
movement
Saturated zone
Components of a typical soil
1) 45% mineral (Si, Fe, Al, Ca, K, Mg, Na)
The two most abundant elements in the earth’s crust are Si
(47%) and O (27%)
Quartz = SiO2
Clay minerals are aluminum silicates
Nonsilicates = NaCl, CaSO4 (gypsum), CaCO3 (calcite)
OM
2) 50% pore space
3) 1 to 5% organic matter
Pore space
Mineral
Soil texture – this defines the mineral particle sizes that make
up a particular soil.
particle diameter
range (mm)
Sand: 0.05 – 2 mm
Silt:
0.002 – 0.05 mm
Clay: 0.0002 – 0.002 mm
Surface to volume ratio
(cm2/g)
50
450
10,000
Texture and pore size distribution
Loam texture
Fine
Coarse
Sand texture
Number of pores
Number of pores
Number of pores
Clay texture
Fine
Coarse
Fine
Coarse
The amount of clay and organic matter in a soil influence the reactivity of that soil
because they both add surface area and charge. Because large amounts of clay
make the texture of the soil much finer, the average pore size is smaller.
Similarly fluids like water move more easily through large pores, not because
the water molecules are too large, but because there is less resistance to
water movement through larger spaces.
Pore size distribution is important when one considers movement of fluids and
of microbes through a porous medium. Protozoa and bacteria will have
difficulty moving through even sandy porous media.
Pore size
5% of the
mean pore
diameter
20 um
0.6-20 um 0.02–0.6 um
Filtration is important when the size of
the bacterium is greater than 5% of the
mean diameter of the soil particles
Organic Matter
The major input of organic matter in soil is from plant, animal, and
microbial biomass. Humus is the ultimate product of degradation of
organic matter. Humus is aromatic in character. This is because the
humus backbone is derived from the heterogeneous plant polymer lignin
which is less readily degradable than other plant polymers (cellulose and
hemicellulose).
Core molecules for
organic humus
Humus has a three dimensional sponge-like structure that can absorb
water and solutes in the water. Humus is only slowly utilized by soil
organisms and has a turnover rate of 1 to 2% per year. In general soils
with higher organic matter contents have higher numbers of microbes and
higher levels of activity.
Humus shares two properties with clay: it is highly charged and it has a
large surface area to volume ratio.
The quantity of organic matter found in soil depends on climate. Soils
found in temperate climates with high rainfall have increased levels of
organic matter. Levels of organic matter found in soil range from essential
no organic matter (Yuma, AZ) to 0.1% organic matter (Tucson, AZ) to 3 to
5% organic matter (midwest) to 20% organic matter (bogs and wetlands).
Bogs and wetlands
Organic matter > 20%
Bogs cover 5 – 8% of the terrestrial surface
Why do peat bogs have very low microbial activity? (see Info Box 4.2)
Surface Soils
10 structure = soil particles + organic matter (humus) + roots +
microorganisms
20 structure = aggregate or ped = stability
Humic-like substances secretion
hydrophobic region
Bacterial colonies
Polysaccharide secretion - hydrophobic region
binding of clay particles
Polysaccharide secretion
binding of clay particles
Fungi
Soil aggregate
Physical entanglement
Cross-section
Clay Particles
C
Polysaccharide secretion
Cell wall
Fissure
Fungal hyphae
MicroNon perturbed clay
environment =
oriented, packed
and glued clay
1 micron
Soil aggregates are formed and stabilized by clay-organic
complexes, microbial polysaccharides, fungal hyphae and plant
roots.
See Info Box 4.4 for a special case of aggregation, cryptobiotic
crusts.
Soil aggregates are associated with relatively large inter-aggregate pore
spaces that range from um to mm in diameter. Each aggregate also has
intra-aggregate pore spaces that are very small, ranging from nm to um in
diameter.
Interaggregateporespace(mtom
minsize) Intraaggregate pore space
(nmtomin size)
Enlargement
Aggregate
particle
Intra-aggregate pores can exclude bacteria (called micropore exclusion).
However, after a spill, contaminants can slowly diffuse into these pores.
This creates a long-term sink of pollution as the contaminants will slowly
diffuse out again.
Just how many pores are there?
Assume a soil aggregate that is 2 x 2
x 2 mm. Further assume that the
volume of the aggregate is 50% pore
space. How many pores of diameter
15 um does the aggregate have?
How many pores of 50 um?
2 mm
2 mm
(the volume of a sphere is: 4/3π r3)
2 mm
Calculation for 15 um pores:
The volume of the aggregate is 2 mm x 2 mm x 2 mm = 8 mm3
Pore space is 50% of 8 mm3 = 4 mm3
A pore of 15 um diameter has volume = 4/3 π (7.5 um)3 = 1.77 x 103 um3
4 mm3 (1000 um)3 / 1.77 x 103 um3 = 2.3 x 10 6 pores of 15 um per aggregate!
mm3
pore
Where are the bacteria?
In soil 80 to 90% of the bacteria are attached to surfaces and only 1020% are planktonic. Cells have a patchy distribution over the solid
surfaces, growing in microcolonies. Colony growth allows sharing of
nutrients and helps protect against dessication and predation or grazing
by protozoa.
Interaction of contaminants and microbes with soil surfaces
Soils have an overall net negative charge that comes from clay oxides,
oxyhydroxides, and hydroxides. The negative charge attracts positively
charged solutes from the soil solution in a process called cation
exchange. Organic matter also provides a net negative charge and
adds to the cation exchange capacity of a soil.
Normally, soil cations such as Na+, K+, or Mg2+ bind to cation exchange
sites. However, when a positively charged metal contaminant such as
lead (Pb2+) or an organic contaminant are present they can displace
these cations. This leads to sorption of the contaminant by the soil.
-
Add
-
-
Cation Exchange
- Na
+
+
Clay particle
-++
+
+
+ +
+
+
+
K
+
+-
+
-
-+
+- - +
-+ --
-+
+
++-+
-+ ++- +
-++
-
++ ++
++ ++
2+
Mg
- + +- +++++
-
+
+
+
- Na+
- ++
+
-+ ++
+
(Metal contaminant)
+++
+
++ 2+
Pb
+
++ +
++
3+
Al
+ +
-+ +++ - +++++
+
- ++
- ++ - ++
Similarly, bacteria are sorbed to soil. In this case the bacterium, which
like the soil has a net negative charge, is sorbed through a cation
bridge.
+
+
-
-
++
-
++
- -
2+
Mg
C la y p a rtic le
n e g a tiv e ly c h a rg e d
Bacterium negatively
charged
++
Divalent cation
---
+
A tta c h m e n t o f b a c te riu m
th ro u g h c a tio n b rid g in g
A second mechanism for sorption of contaminants is hydrophobic
binding. Hydrophobic sites on the soil surface are created when
organic matter is present. Polar groups in the sponge-like organic
matter structure face the outside while non-polar groups are in the
interior of the sponge. Nonpolar molecules are attracted to the
nonpolar sites in the organic matter resulting in hydrophobic binding.
Organic matter
Nonpolar
organic molecules
Clay
The soil solution is a constantly changing matrix composed of both organic
and inorganic solutes in aqueous solution.
Fertilizers, pesticides
spilled fuel, and
irrigation runoff
Soil Solution
++
+ +
+-
-+
+
-
+
++
++
-
++
++
+ +
+
++
+
++
++ +
+ +
++
++
++
++
++
+ +
++
+++ + +
+
+
++
+
+ +
+ +
+ +
+
+
+
-+ -
+
+ +
-
- -+ - - - - - -
P
PP
+
PP
PPP
PPP PP
- +-
PPPPPP
PP
+
+
PPPPPP
PP
++ +
+ +
PPPPPPP
P
+ + P
++
+
PPPPPPP
PP
+ +
+
PP
P
+
+ PP+PPP+P+
++
+ +
+
PPPPPPP
PP
+
+ + ++
PPPPPPP
P
+
P
+ +
++ +
PPPP
PPP
PPP PP
- + + -+ +
+ -+
-
++
+ +
+ +
+ +
+
+ +
+ +
++ + +
++
++
++
PPPPPP
PP
Cation exchange
++
++
++
PPP
PPP PP
-
+ +
+
+ +
+-
+
+ +
+
+ +
+ +
+ + + +
+ + + ++ +
+ ++ + +
++
++
+
++
++
++
++
+
++ ++
+ + +++
+
PPPPPP
PP
-
-
++
PPPPPP
PP
+
+
-
++
+ +
++
++
PPPPP
PPP
+
+ +
+ +
+ +
PPPPPP
PP
++ +
++
+ +
++
++
PPPPPP
PP
++
PPPPPP
PP
++
PPPPPP
PP
PP
++
++
+
+-+ +
PPPP
PPPP
PP
-
Plant roots
+ +
++
PP
PPPP
PP
PP
+
+
++
PPP
PPPP
P
PP
+
-
+ +
++
PPPPPP
PP
PP
+ ++
+
PPPPPP
PP
PP
Precipitation from solution
and parent minerals
+
Microorganisms
Water movement and soil water potential
Increasing distance from particle surface
m
A
Soil water potential depends on
how tightly water is held to a soil
surface. This in turn depends on
how much water is present.
Capillary forces have water
potentials ranging from –31 to
–0.1 atm. Optimal microbial
activity occurs at
approximately -0.1 atm.
At greater distances there is
little force holding water to the
surface. This is considered
free water and moves
downward due to the force of
gravity.
Capillary forces
Soil particles
Surface forces have water
potentials ranging from –
10,000 to –31 atm.
Surface forces
Soil air
FREE WATER
Gravitational
forces
Soil air
0%
% Saturation of
the soil pore
100%
Soil atmosphere
The composition of the earth’s atmosphere is approximately 79%
nitrogen, 21% oxygen, and 0.03% carbon dioxide. Microbial activity in
the soil can change the local concentration of these gases especially in
saturated areas.
Composition (% volume basis)
Location
Nitrogen (N2)
Oxygen (O2)
Carbon Dioxide (CO2)
Atmosphere
78.1
20.9
0.03
Well-aerated surface soil
78.1
18 - 20.5
0.3 – 3
Fine clay/saturated soil
>79
0 - 10
Up to 10
Microorganisms in soil – an overview
• minor role as primary producers
• major role in cycling of nutrients
• role in soil formation
• role in pollution abatement
Numbers and types of microbes in typical surface soils
Bacteria
Culturable counts 106 – 108 CFU/g soil
Direct counts
107 – 1010 cells/g soil
Estimated to be up to 10,000 species of bacteria/g soil
Highest
numbers
Actinomycetes
Culturable counts 106 – 107 CFU/g soil
Gram Positive with high G+C content
Produce geosmin (earthy smell) and antibiotics
Fungi
Culturable counts
105 – 106/g soil
Highest
biomass
Obligate aerobes
Produce extensive mycelia (filaments) that can cover large areas.
Mycorrhizae are associated with plant roots.
White rot fungus, Phanerochaete chrysosporium is known for its ability to
degrade contaminants.
Comparison of bacteria, actinomycetes, and fungi
Numbers
Bacteria
Actinomycetes
Fungi
highest
intermediate
lowest
Biomass
Cell wall
--- similar biomass ---
--- PEP, teichoic acid, LPS ---
largest
chitin/cellulose
Competitiveness
for simple organics
most
least
intermediate
Fix N2
Yes
Yes
No
Aerobic/Anaerobic
both
mostly aerobic
aerobic
Moisture stress
least tolerant
intermediate
most tolerant
Optimum pH
6-8
6-8
6-7
Competitive pH
Competitiveness
6-8
all soils
>8
dominate dry,
high pH soils
<5
dominate
low pH soils
Bacterial numbers and activity in surface soil, the
vadose zone, and the saturated zone
Example 1: A shallow core
Konopka and Turco (1991) compared microbial numbers and activity in a
25 m core that included surface soil, vadose zone, and shallow saturated
zone samples.
Site was a 40 year old corn field at Purdue University
?
Surface soil
?
Vadose zone
?
Shallow saturated zone
0
5
5
10
15
20
25
A
A
5
Depth (m)
0
Depth (m)
Depth (m)
0
A
10
Compare
the microbial numbers
in the 15
surface, vadose zone, and
20
saturated
regions.
25
10
15
20
25
0
50
25
75 600
800
-3
0
50
25
0 75 600
25 800
50
-3
75 600
Culturable
counts (10(10
CFU/g)
-3 CFU/g)
Culturable counts (10
Culturable
counts
-3
800
Culturable counts (10 CFU/g)
CFU/g)
B
0
15
25
Depth (m)
B
0
Depth (m)
Depth (m)
0
15
15
25
0
25
0
5
10
0
7
15
5
10
5
5
20
25
7
200
400
C
0
C
5
10
10
15
15
20
20
25
0
25
0
15
-7 cells/g)
AODC (10
AODC
(10cells/g)
Depth (m)
0
Depth (m)
0
15
10
AODC (10 cells/g)
15
C
10
5
7
AODC (10 cells/g)
Depth (m)
B
06 00
800
200
400
6 00
200
800
400
6 00
Phospholipid g/g
Phospholipid
(ug/g)
800
Surface soil sample
80
glucose
phenol
60
evolved as a % of the carbon added
1) lag time
2) growth rate
3) cell yield.
14CO
2
Compare the microbial
activity in the three
regions in terms of:
40
20
0
0
8
16
24
32
Vadose zone sample
80
60
40
20
0
0
8
16
24
32
80
60
40
Saturated zone sample
20
0
0
8
16
Days
24
32
Example 2: The deep vadose zone
A 70 m core was taken in the Snake River Plain in Idaho (Colwell, 1989).
Compare the direct and culturable counts between the surface samples
and the deep vadose zone samples.
TABLE 4.11 A comparison of microbial counts in surface and
70-m unsaturated subsurface environments
Sample site
Direct
counts
(counts/g)
Culturable
counts
(CFU/g)a
Surface (10 cm)
2.6 × 106
3.5 × 105
Subsurface basalt-sediment
interface (70.1 m)
4.8 × 105
50
Subsurface sediment layer
(70.4 m)
1.4 × 105
21
aCFU,
colony-forming units.
Example 3: The deep saturated zone
In 1987, a 470 m core was taken in the southeast coastal plain in South
Carolina (Fredrickson et al., 1991). Culturable counts ranged from 103 to
106 CFU/g in a permeable sandy sample retrieved from between 350 and
413 m. Culturable counts were lower (non-detect to 104 CFU/g) in a low
permeability sample taken between 450 and 470 m.
More recently, (2001-2006), a series of water samples were taken from
the saturated zone at depths of 0.72 - 3 km in the Witwatersrand Basin
in central South Africa ( Gihring et al ., 2006 ). Total microbial numbers
in the samples were estimated to be as low as 103 cells/ml. Diversity
was low as shown by analysis of the 16S rRNA gene, which generated
only an average of 11 bacterial OTUs from all the samples. Compare
this to surface soils that have up to 6300 OTUs!
Compare the microbial counts measured in surface, vadose
zone, and saturated zone samples presented in the 3 examples.
What do these counts imply for activity in each of these regions?
What do these counts imply for diversity in each of these
regions?
Summary and Reality Check
Despite the fact that there are microbes present in most subsurface
samples, often in high numbers, the level of microbial activity in the deep
subsurface is very very low when compared to activity in surface soils or
in lake sediments.
1
-3
10
10-5
-9
10
-13
Su
aq bsu
uit rfa
ar ce
d
De s
z o ep
ne va
s do
se
De
or ep
se con roc
dim so ks
en lida
ts te
d
10
Su
so rfac
ils e
La
se ke
dim
en
De ts
se ep
dim se
en a
ts
Su
aq bsu
uif rfa
er ce
s
Rates of CO 2 production
(moles/liter/year)
10