Objectives:

1
Chapter 4 - The Terrestrial Environment

• Objectives
• Understand the terrestrial environmental from an
  integrated physical, chemical and biological
  perspective.
• Define a surface soil, the vadose zone, and the
  saturated zone.
• 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.
• Understand how soil water potential relates to
  microbial activity.
• Understand the basics of contaminant sorption and
  microbial sorption.
• Understand how microbial activity can influence
  the soil atmosphere.
• Be able to describe the types, numbers, and
  relative activities of microbes found in surface
  soil, vadose zone, and saturated zone
  environments.
• Discuss the respective competitiveness of the
  bacteria,
• actinomycetes, and fungi in soil.

2
Surface soils Vadose zone Saturated
zone shallow aquifers intermediate
aquifers deep aquifers
3
Components of a typical soil
1) 45 mineral (Si, Fe, Al, Ca, K, Mg, Na)
The two most abundant elements in the earths
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
Mineral
Pore space
4
Soil texture this defines the mineral particle
sizes that make up a particular soil.
particle diameter
Surface to volume ratio
range (mm) (cm2/g)
Sand 0.05 2 mm 50 Silt 0.002
0.05 mm 450 Clay 0.0002 0.002
mm 10,000
5
Texture and pore size distribution
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.
6
Pore size 5 of the mean pore diameter
20 um
0.6-20 um
0.020.6 um
Filtration is important when the size of the
bacterium is greater than 5 of the mean diameter
of the soil particles
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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.
8
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 gt 20 Bogs
cover 5 8 of the terrestrial surface
Why do peat bogs have very low microbial
activity? (see Info Box 4.2)
9
Surface Soils
10 structure soil particles organic matter
(humus) roots

microorganisms
20 structure aggregate or ped stability
10
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.
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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.
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.
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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? (the volume of a sphere is 4/3p r3)
2 mm
2 mm
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 p (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
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Where are the bacteria?
In soil 80 to 90 of the bacteria are attached to
surfaces and only 10-20 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.
14
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.
15
Cation Exchange
16
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.
17
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.
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The soil solution is a constantly changing matrix
composed of both organic and inorganic solutes in
aqueous solution.
Soil Solution
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Water movement and soil water potential
Soil water potential depends on how tightly water
is held to a soil surface. This in turn depends
on how much water is present.
Surface forces have water potentials ranging from
10,000 to 31 atm.
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.
20
Soil atmosphere The composition of the earths
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.
21

• Microorganisms in soil an overview
• minor role as primary producers
• major role in cycling of nutrients
• role in soil formation
• role in pollution abatement

22
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 Actinomycetes Culturable
counts 106 107 CFU/g soil Gram Positive with
high GC content Produce geosmin (earthy smell)
and antibiotics Fungi Culturable counts 105
106/g soil 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.
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Comparison of bacteria, actinomycetes, and fungi
Bacteria Actinomycetes Fungi Numbers highes
t intermediate lowest Biomass ---
similar biomass --- largest Cell wall ---
PEP, teichoic acid, LPS --- chitin/cellulose Comp
etitiveness most least intermediate for
simple organics Fix N2 Yes Yes No Aerobic/Ana
erobic both mostly aerobic aerobic Moisture
stress least tolerant intermediate most
tolerant Optimum pH 6-8 6-8 6-7 Competitive
pH 6-8 gt8 lt5 Competitiveness all
soils dominate dry, dominate
high pH soils low pH soils
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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
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Compare the microbial numbers in the surface,
vadose zone, and saturated regions.
26
Compare the microbial activity in the three
regions in terms of 1) lag time 2) growth
rate 3) cell yield.
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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.
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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?
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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.