Tools should be easy to use
marking depth on a shovel or
spade will make it easy.
Square ended spades are
great for earthworms.
Soil Microarthropods
Watrer Stable aggregates
Another way to recycle and learn
at the same time.
Photo by V. Behan-Pelletier AAFC
Indirect measures of soil biology
Indirect measurement is all based on
activity
% active organic matter
mineralisation
respiration
Sol Vita test measures soil respiration and
N mineralization in one test!
Li Corr portable gas chromatograph for measuring CO2 that comes from the soil
Sol Vita test is the cheaper and easier way to measure soil respiration and N
mineralization and you can do it on the farm.
Sol Vita test is the cheaper and easier way to measure soil respiration and N
mineralization and you can do it on the farm.
Ways of studying the microbes
that live in soil
Plate and then count
Stain and then look in the microscope and
count
Biolog- physiological profiling
Genetic profiling
PCR - Polymerase Chain Reaction
DGGE – Denaturing Gradient Gel
Electrophoresis
Lipid Analysis- FAME and PLFA
Why FAME or PLFA?
Fatty Acid Methyl Esters (FAME) are made from all
lipids that are extracted from the soil (living or not).
Phospholipid fatty acids (PLFA) are unique to the
membranes of living cells.
PLFAs deteriorate quickly upon death so they indicate
living biomass.
Each of the major groups of organisms such as
bacteria, fungi, protozoa, nematodes have unique
PLFAs or markers that allow us to examine the amount
of living biomass of each group in the soil.
In the beginning
1590 two Dutch spectacle makers, Zaccharias Janssen and his father
Hans started experimenting with these lenses. They put several
lenses in a tube and made a very important discovery. The object
near the end of the tube appeared to be greatly enlarged, much larger
than any simple magnifying glass could achieve by itself! They had
just invented the compound microscope (which is a microscope that
uses two or more lenses).
Anthony Leeuwenhoek of Holland (1723) was the first to describe
bacteria and protozoa – animacules.
Plating, staining, microscope
We know that plating soil onto growth media probably only shows us >1% of
the microbes in the soil.
Ways of studying the microbes
that live in soil
Plate and then count
Stain and then look in the microscope and
count
Biolog- physiological profiling
Genetic profiling
PCR - Polymerase Chain Reaction
DGGE – Denaturing Gradient Gel
Electrophoresis
Lipid Analysis- FAME and PLFA
Why FAME or PLFA?
Fatty Acid Methyl Esters (FAME) are made from all
lipids that are extracted from the soil (living or not).
Phospholipid fatty acids (PLFA) are unique to the
membranes of living cells.
PLFAs deteriorate quickly upon death so they indicate
living biomass.
Each of the major groups of organisms such as
bacteria, fungi, protozoa, nematodes have unique
PLFAs or markers that allow us to examine the amount
of living biomass of each group in the soil.
Continued
Microorganisms modify their cell
membranes depending on growth stage
and environment. The amount of
saturated PLFA compared with unsaturated
PLFA can tell us about the stress in a
microbial community. The amount of
precursors compared to the end product of
PLFA can tell us where a microbial
community is in terms of the growth curve.
 Hydroxylated PLFA are closely associated
with legume inoculants and plant growth
promoting rhizobacteria (PGPR).
 Changes in the amount of overall microbial
biomass are directly related to the turnover
of organic matter.

Carbon chains are the backbones
Fatty acids with 20 or less carbons are
markers for bacteria, fungi, protozoa.
Ahhh another source of C in the soil
How we get the PLFA
Soil sample
Extracted
Saponified
Solid phase
separation
Neutral acids
Glycolipids
Phospholipids
/
What a microbial PLFA community looks like from the
perspective of the Gas Chromatograph (GC). The numbers
are retention time.
Going from data to Results
The data from the GC is then put into a
program that calculates amounts based on
dry weight of soil, sorts the peaks into
specific marker PLFA (that indicate specific
groups of organisms), and then puts the
data into a table. So you can compare the
profiles for each of your soils.
In Search of Results
It is important to sample every soil you
want to compare at the same time. For
example if we want to compare various
cover crop mixtures; we would sample
each plot or field area at the same time.
We do this because:
There is no baseline for soil microbiology
Total PLFA
12000
PLFA ng/g dry wt soil
10000
8000
6000
4000
2000
0
Roggan
Roggan Cultan Raps mitt Vlee
Maiz links
Treatment
Maiz mitt Wecht
Unknown
Actinomycetes
800
PLFA (ng/gdrywt)
700
600
500
400
300
200
100
0
Roggan
Roggan
Cultan
Raps mitt
Maiz links
Vlee
Treatment
Maiz mitt
Wecht
Unknown
Total PLFA
3000.00
2500.00
2000.00
1500.00
1000.00
500.00
0.00
soybean
switchgrass
NT corn
Fescue h
ES Fescue
Pred
40
35
30
25
20
15
10
5
0
25
20
15
PC17
10 PC19
5
0
soybean
switchgrass
NT corn
Fescue h
ES Fescue
B:F
25
20
15
10
5
0
soybean
switchgrass
NT corn
Fescue h
ES Fescue
AMF
120
100
80
60
40
20
0
soybean
switchgrass
NT corn
Fescue h
ES Fescue
Actin
350
300
250
200
150
100
50
0
soybean
switchgrass
NT corn
Fescue h
ES Fescue
Sat:Mono
2.15
2.1
2.05
2
1.95
1.9
1.85
1.8
1.75
1.7
1.65
Mono:Poly
45
40
35
30
25
20
15
10
5
0
So what does this mean for a
farmer?
Test products
 Examine the affects of cover crops, manure,
herbicide, insecticide and etc.
 Fertilizer affects on mycorrhizae

 Farmers
can make an informed decision!
Ward Laboratories and Rhizoterra have
the sampling procedures on their web
sites.
If you want interpretation or help
interpreting the test label your sample with
Rhizoterra so the lab will send your results
to me in the format I need to run my
analysis.
Indirect measures of soil biology
Indirect measurement is all based on
activity
% active organic matter- Walkley-Black
mineralisation
respiration
Sol Vita test measures soil respiration and
N mineralization in one test!
Li Corr portable gas chromatograph for measuring CO2 that comes from the soil
What is soil respiration?
Soil Respiration occurs when organic carbon (C) is
released from the soil as CO2. Plant take up CO2 from
the atmosphere and during photosynthesis convert the
CO2 to carbon compounds such as carbohydrates and
cellulose. Plants use these carbon compounds to build
structural components such a lignin, or respire them to
release energy. Over time plants die and the structural
components are decomposed by heterotrophs –
organisms that cannot fix carbon, and use organic
carbon for growth. As heterotrophs use the organic C
they release CO2, and we call this soil respiration. Root
activity can add to over all soil respiration. As
heterotrophs release the C they also release N, P, S and
any other elements that are attached to the C-chains the
heterotrophs are consuming. Heterotrophs can be
bacteria and fungi, and the soil fauna. Predators are the
ultimate heterotrophs.
More about decomposition………..
Most people associate decomposition with the disappearance or
breakdown of organic residues or litter
 a complex interaction between both microbes (eg bacteria and
fungi) and soil fauna (eg mites, collembola, and earthworms).
During the process of decomposition elements are being transformed
from organic to inorganic forms- mineralized into forms for plant
uptake or microbial use.
Cellulose compounds make up more than 50% of the carbon (C) in
plant residues providing the fuel for the microbial mineralization of
nitrogen (N) and phosphorus (P).
In the rhizosphere, root exudates and dead root cells provide the
microbial fuel for mineralization. When the soil biota (everything that is
alive in the soil) are given quality residues (including root exudates)
under ideal conditions of soil moisture and temperature, there is a lot
of respiration happening.
Soil respiration is directly related to the availability of carbon, nitrogen
and other mineral nutrients- or the quality of the organic residues
So you can see how it could be possible to use soil respiration as an
indicator of soil health and fertility.
Sol Vita test is the cheaper and easier way to measure soil respiration and N
mineralization
Calculations for Sol Vita Test
Active Carbon, ppm = total CO2-C as
found in the 24h reading.
Biomass Carbon, ppm = total CO2-C
from LCD x 20
Est Mineralizable-N= total CO2-C x
0.5 = lbs/ N / acre for current growing
season).
N- Mineralization
In the soil, nitrogen exists as a component of the gas
(N2) between soil pore spaces, or in an organic form
such as plant and microbial proteins and amino acids
in the SOM. The process that converts organic N in
SOM to plant and microbe useable forms of
inorganic N such as ammonium (NH4+) and nitrate
(NO3-) is called mineralization. The process of
mineralization is performed primarily bacteria and
fungi. Climate and soil type including the microbial
community influence the dynamics between organic
and inorganic N. Soil moisture and temperature can
limit or optimize the activities of soil microorganisms.
Soil temperature below freezing and above 80oF limit
microbial activities. Soils that are too dry will also
have less microbial activity.
N mineralization is closely tied to the carbon (C)
cycle, because decomposing microorganisms get
their energy from carbon compounds in SOM.
Carbon and N compounds in SOM can be
classified as labile (active), and a stabilized
(passive). The labile pool is composed of microbial
biomass, particulate organic matter (fine plant
residues), and compounds that are readily
decomposed by soil microorganisms. The
stabilized pool of organic matter is composed
primarily of complex stable organic compounds
that are resistant to microbial decomposition. Over
the long term, because it provides the underlying
food source for soil microorganisms, the stabilized
SOM is an important source of slowly
mineralizable N.
• Nitrogen mineralization is a measure of soil quality: soils with high N
mineralization potential tend to be inherently fertile, while soils with
low N mineralization potential tend to be less fertile and require
greater agricultural inputs.
• Extensive cultivation with minimal organic matter input depletes soil
organic matter, causing a significant decline in the potential for N
mineralization processes to provide plant-available N
• Organic inputs increase the potential for N mineralization to contribute
to plant nutrition.
• Soils will higher rates of respiration, tend to have more microbial
biomass, better soil structure, and higher levels of quality organic
matter.
• Soil respiration can be used as an indicator of soil health and quality,
in combination with a number of other soil processes.