Microorganisms and Soil Health
Kura clover on Menfro silt loam in
Chariton County, Missouri 2006
Doran et al. 1994.
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Microbial groups are associated with other soil health indicators
Active C
Nmin; Nitrate,
Ammonium.
P mineralization,
solubilization
Nmin
Aggregate
Stability
Microbial involvement in stable aggregate formation
1)
Microfauna (< 0.1mm), protozoa
2)
Mesofauna (0.1 - 2mm),
- mites, collembolans,
and nematodes
3)
Macrofauna
(>2mm),
(oligochaetes
earthworms).
Biological Attributes of Soil Health
Importance:
Biological activities in soils:
Highly sensitive to soil-altering processes (degradative or beneficial);
Changes can guide appropriate management (conservation or restoration
practices in response to degradation; validation of GMP in practice)
Indicators: measures that collectively suggest whether or not soil is functioning
normally
Development / identification of a standard set of biological soil health indicators has
been elusive.
Major difficulty in use organisms and activities to assess soil health =
methodological.
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Microbial Ecology Interactions
SOIL - Biologically dynamic system
Biological attributes interact with physical and chemical properties
• Aggregate Stability
activity and products of organisms contribute to aggregation; water
transport, low erosion, microbial habitat, C storage
• Soil Organic Matter (C fractions)
key factors influencing biological activity and result of microbial
activity, soil structure, soil fertility, plant nutrition
• Soil Enzyme Activity
Soil microbial activity, nutrient transformation, decomposition;
influenced by soil nutrient status, vegetation, management
Microbial Indicators of Soil Health
Microbial Biomass – very general indicator
Enzyme Activities
Soil Respiration, N transformations (‘Greenhouse gasses’?)
C Utilization Profiles
Fatty acid Profiles
Nucleic Acid Profiles
Selected “soil fauna”
*ORGANIC MATTER (CARBON)
– influences many readily measurable soil functions and processes; soil
microorganisms closely associated w/ “active fraction of SOM”
*Aggregate Stability
*Intimately related to soil biological processes
No consensus in defining specific parameters for inclusion in data set for Soil Health assessment
Complete data set on microbial portion of Soil Health is lacking
Need: Identify minimum number of parameters that considers processes as well as community
diversity for successful establishment of biotic component in determining Soil Health
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Few Biological Indicators can be Field Measured -Soil respiration (CO2 efflux) - indicator of biological activity (SQI 2001)
Draeger Tube - color change shows relative amount CO2
(appropriate conversion factor(s) allow calculation of soil
microbial biomass C)
Microbial biomass => indicates potential ‘turnover’ rate relative to
amount of N mineralized - tends to decline under degradation
Solvita “Soil Life Kit” - gel indicator
color change (24-hr incubation),
qualitative indicator of respiration;
expensive
10
11
Phospholipid Fatty Acid Methyl Ester (PFLA)
•PLFA found only in living cells – PFLA profiles provide measure of soil microbial
diversity
•Specific PLFA patterns detected via gas chromatography yield information on soil
microbial community shifts and structure
•“Peaks” indicate “biomarkers” for specific soil microbial groups
http://www.microbe.com/plfa.html
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Unger et al. 2013. Agroforestry Systems
Carbon chain lengths of 12-20 carbons are generally associated with microorganisms. Fatty acids
designated by the number of carbon atoms, followed by a colon, the number of double bonds, and
then position of the first double bond from the methyl (ω) end of the molecules. Branched fatty acids
are indicated by ‘i’ and ‘a’ for iso and anteiso branching, respectively.
How can Soil Microbial status of soil be expressed?
1. “Total Living Microbial Biomass” ng/g, nmol or pmol units
Example: 1400 - 6700 ng/g soil for 240 Missouri soybean fields
Implications:
“Soil Microbial Biomass”
• Labile (living) component of the soil organic fraction
• 1 – 3% of the total soil organic C
• ≤ 5% of the total soil N
• Contributes to potential Nmin pool: [30 - 60 lbs/A for SOM 2.65 - 5.3%]
• “activity” is mediated by the diverse soil microbial community
• Involved in nutrient fluxes, decomposition, plant growth regulation
• Sensitive indicator of changes in managed and natural ecosystems –
major soil quality/health parameter
• No indication of function or activity
How can Soil Microbial status of soil be expressed?
2.“Diversity Index” A diversity index is a quantitative measure that reflects how many different
types (such as microbial species - ‘biomarkers’) are present in sample.
Index value increases when number of types increase and evenness (how
close in numbers each species in an environment are) increases.
Index value is maximized when all types are equally abundant.
Diversity index ranged from 1.5 to 3.5 for soils from 240 Missouri soybean
fields (2011).
-Similarity index: comparing the similarity of soils
-Implications:
- High of soil microbial diversity assures functional activity is near optimum
- (activity of microbial ‘consortia’ in place)
Indices for describing soil microbial abundance and diversity
Values reflect microbial community characteristics
Diversity index (various) - assess composition diversity
Species richness (abundance) - numbers of different species
Species evenness - distribution of individuals within species
Greater diversity => greater ability of soil to accommodate all critical
functions necessary for healthy condition
Certain Management (i.e., Cover Cropping, Managed Grazing, etc.) can
foster Biodiversity Reduce externalities (inputs)
Reduce pollution
Benefit vegetative and soil biological diversity
*Use of diversity measurement in Soil Health assessment is still in flux
Soil Quality (Health) concept advanced in early 1990’s
Soil microbial diversity beginnings in 1980’s but is constantly
evolving to present day We have opportunity to demonstrate value of this indicator to overall
soil health assessment
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Soil Microbial Categories:
3. “Total Bacteria” (ng/g; nmol/g, pmol/g, mol%)
- Gram negative
Overall: plant health, nutrient cycling
N transformations:
N2 fixation (rhizobial, endorhizal, associative)
Nitrifying bacteria
Denitrifying bacteria
Pseudomonads - nutrient mobilization, disease suppression
- Gram positive
Overall: decomposition of complex organic materials (relative to Gram -)
stress resistance
Actinobacteria - disease suppression (antibiotic synthesis); residue
decomposition
- Anaerobic bacteria
function in saturated microenvironment - denitrification, sulfate
reduction;
Indicators of soil compaction or aeration problems - related to DB values
Antifungal activity of bacterial isolates
Soil Microbial Categories:
4. “Total Fungi” (ng/g; nmol/g, pmol/g, mol%)
- Overall: Decomposers of most complex
organic substrates and xenobiotics
Ammonification
Soil aggregation
Pathogen suppression
- Mycorrhizal fungi - plant symbiosis; mineral and organic P
mobilization & transport to plant; improves root water uptake
(impart drought resistance
to plant); mineralize N, S, K;
Pathogen suppression;
‘Glomalin’ deposits in
rhizospheres are critical
sinks for C storage and for
stable soil aggregation
Faculty of Biology Genetics, University of
Munich
Soil Microbial Categories:
5. “Protozoa or Protists” (ng/g; nmol/g, pmol/g, mol%)
- Overall: Nutrient cycling
- Predatory - ‘microbial turnover’ - mineralize organic, microbial
N
maintains balanced microbial community
Soil Microbial Categories:
6. Algae (ng/g; nmol/g, pmol/g, mol%)
- Overall: Nutrient cycling; photosynthesis (C supply to soil and
microbial community); extracellular polysaccharides bind soil
particles, increase aggregate stability, formation of erosion-resistant
soil crusts; food source for predatory protozoa, nematodes
- ‘microbial turnover’
Nostic sp.
Soil Microbial Categories:
7. Nematodes
Important in regulating bacterial and fungal communities; cycle N;
primary decomposers of coarse organic materials
Location of symbiotic bacteria in intestines of their respective nematode hosts. (A) Xenorhabdus nematophila
cells located in the intestinal vesicle of Steinernema carpocapsae infective juveniles. (B) Photorhabdus
luminescens cells located in the anteriors and midintestine of Heterorhabditis bacteriophora nematodes. The
bacteria are denoted by arrows.
Soybean Cyst Nematode
Eggs
Stylet (feeding structure)
Cysts on soybean root
Cysts on Roots
SCN egg attacked by soil fungus
Soil Microbial Categories:
8. Soil Insects – Microarthropods
Fragment coarse organic residues, preparing it for subsequent decomposition by
microbes; aid soil structure; feed on plant pathogenic fungi
“Microarthropod” – Collembola – “springtail”
≤ 2.0 mm length
Soil Microbial Categories:
9. Earthworms
Fragment coarse organic residues, preparing it for subsequent decomposition by
microbes; aid soil structure by increasing porosity and aggregation; concentrates soil
N and P in castings; provides gut habitat for microbes involved in mineral cycling;
**Sensitive to changes in soil management
Soil Microbial Categories:
10. “Fungi-Bacteria Biomass Ratio” (F:B) Implication:
Ratios reflect ecosystem:
F:B = 0.3:1 - 0.8:1 => row
crops, vegetables
= 10:1 - 50:1 =>
orchards, woody plants
Fungi may be associated with higher soil NH4;
Bacteria associated with high soil NO3
Certain plants favor specific type of N
i.e., woody plants – NH4
annual plants - NO3
Willow prefers N as NH4
Soil Microbial Categories:
11. “Stress Ratios” i.e., monounsaturated PLFA :
polyunsaturated PLFA or
“saturated PLFA :
monounsaturated PLFA”
higher ratio suggests microbial
community subjected to some
stress; may include plant stress
Microbial diversity components for management practices on
claypan soil, Novelty, MO - 2009 (Buffers established in 1997)
*Microbial biomass did not differ significantly among management practices
Unger et al. 2013. Agroforestry Systems 87:395-402.
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Soil Enzyme Activities as Indicators of Soil Quality
Enzyme activities seem to be sensitive in discriminating among soil management treatment
effects – more dynamic measure vs SOM
Long-term Cropping Sites
Rotations
Tillage Systems
Forest ecosystems -- little effort
Clear-cut sites -- phosphatase activity decreased under compaction vs 'rehabilitated site'
Phosphatase activity inversely proportional to Bulk Density
Suggest soil enzyme activity used by forest managers to identify beneficial management
practices before investigating subsequent tree growth
Selected Soil Enzymes — potential SQ indicators
**Enzymes representing critical soil biological processes should be selected
Enzymes procedures simple, rapid, can be routinely performed - IN THE LAB
Sensitive to temporal changes in soils due to environment or management
Information of long-term effects of management can be provided
Example of activity
indicator detecting
change due to
management well in
advance of SOC
indicator
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Relationship of soil microbial activity to SOC content in Sharpsburg silt loam
Organic farm site in Clay County, MO - SOM annually built up thru organic amendments
GLUCOSAMINIDASE X SOC
400
y = 3.9688x + 42.219
R² = 0.6286
Gluco Activity (PNP/g soil)
350
300
250
200
Continuous vegetative cover
150
100
50
Tilled, not managed
0
0
10
20
30
40
50
60
70
SOC (g/kg soil)
Kremer & Hezel, 2013. Renewable Agric. & Food Syst. 28:245-254.
Expect relationship to improve using specific C fractions vs broader SOC values
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Management Inferences from Soil Health Analysis
Mycorrhizae
Cover crop composition (mix)
stimulates soil mycorrhizae
populations for colonization of
subsequent cash crops
PLFA biomarker
for mycorrhizae
Lehman et al.,
2012