Management Impacts on Soil Microbial Nitrogen Cycling
1. Management Impacts on Soil Microbial Nitrogen Cycling
K. Thompson, BSc, PhD
February 12 2019
karenthompson@trentu.ca
@KarenAshleyTee
2. My Background
• BSc Honours in Environmental Sciences,
UWO (2007)
• Sewoon Foreign Academy and Chosun
University, Gwangju, S. Korea (2007-2009)
• Japan, SE Asia, Russia, England, Costa Rica
(2010)
• PhD at the University of Guelph, in the
School of Environmental Sciences (Land
Resource Sciences) (2016)
• Postdoc at the University of Alberta, in the
faculty of Agriculture, Life and
Environmental Sciences (2016-2017) 2
3. Current and Upcoming Projects
in the ASH Lab at TrentU
• “Regenerative Agriculture in Action” – Intercropping
Demo Plots (OSCIA) (Matt Porter)
• “Feeding soil with agri-food waste” – Abbey Gardens
partnership (E. Stewart, R. Chan)
• “Insect biodiversity in hedgerows” (D. Beresford, A.
Kasaree)
• “Integrated pest management in greenhouse
floriculture” (D. Beresford, B. Foster)
• “Feasibility of small-scale farming to increase
sustainability in Jamaica” (M. Classens, M. Beerman)
• Impacts of Cropping Systems Management and
Climate Change on Microbial C and N – TBD ☺
4. What is Sustainable Agriculture?
→Agricultural production
systems that produce food, fuel
and fibre in an ethical,
responsible, and efficient
manner that conserves
biodiversity and the surrounding
environment, produces healthy
food, is profitable for producers,
and promotes valuable
ecosystem goods and services.
4
6. Challenges for Sustainable
Agricultural Systems
→Increasing population’s needs for food, fuel,
fibre
→Pest, pathogens
→Changes in land management, LUC
→Reduction in cropping system diversity
→Climate change
6
8. Biological
Indicators of
Soil Health
PHYSICAL
Soil Type
Structure and
aeration
Water
infiltration and
retention
CHEMICAL
Available
nutrition
Optimal pH
BIOLOGICAL
Diversity
Nutrient Cycling
Disease /pest
suppression
SOIL HEALTH
17. How do we study soil microbial communities?
1. Collect soils
2. Extract nucleic acids
3. Use molecular methods
DNA = “Who’s there”
RNA = “Who’s potentially
active”
18. Flow of Genetic Info
• DNA = “Who’s there”
• RNA = “Who’s potentially active”
22. Residue Management Influences SMCs
22
Standing Miscanthus
Before Spring Harvest Residue Return After Spring Harvest in Miscanthus
Plots
23. Residue Return Increased N2O Mitigation Potential
nosZ cDNA (transcript abundance)
+R -R N
lognosZtranscriptcopypergramdrysoil
2.0
2.2
2.4
2.6
2.8
3.0
3.2
3.4
23
N2O
Consumption
Thompson, K. A., Deen, B. & Dunfield, K. E.
Appl. Soil Ecol. 130, 79–83 (2018).
24. Project Summary • Miscanthus produces large yields in variable Ontario
climatic conditions.
• Soils under miscanthus supported significantly higher
nosZ gene abundances (larger N2O-reducing
communities) than the traditional land use of corn-
soybean.
24
25. Soil microbial communities
as potential regulators of in
situ N2O fluxes in annual
and perennial cropping
systems
*Thompson, K. A., Bent, E., Abalos, D.,
Wagner-Riddle, C., and K. E. Dunfield. Soil
Biology and Biochemistry 103 (2016) 262-
273
26. Context of Study
•Perennial and annual
crops provide varied C
and N inputs
•Liquid dairy manure
(LDM) added to soils
provides C for
denitrification and organic
N and NH4-N that can be
nitrified.
27. Objective and Research Questions
Are N-cycling microbial community size or structure affected by:
•Perennial vs. annual cropping systems
•LDM management in annual cropping systems
•Ploughing in perennial cropping systems
…and if so do these differences relate to N2O fluxes over time?
28. Field Comparisons
•Perennial vs. Annual Systems
•LDM application timing in Annual
Systems
•Ploughing in Perennial System
28
Hay ploughed October 2013
Corn: approx. 135 kg N ha-1 liquid dairy manure, November or April,
(Starting Fall 2011)
Hay: approx. 90 kg N ha-1 liquid dairy manure, June (Starting Spring
2012)
=PH
=FMC
=SMC
29. Methods
• Soil collected along transects in 2012 and 2014.
• DNA extracted from soil
• qPCR used to enumerate nitrifier and denitrifier
gene abundances
• Gene amplicon libraries prepared and amplicons
sequenced (MiSeq), resulting sequences clustered
into OTUs
Gene Targets:
• Denitrifiers = nirS, nirK and nosZ
• Nitrifiers = amoA and crenamoA
39. Project Conclusions
• Distinct N-cycling communities were associated with land use and
management.
• Shifts in N-cycling microbial communities demonstrated relationships
with agricultural management, which were associated with differences in
N2O flux.
• The size of the N2O-reducing community (nosZ) and specific OTUs may
be largely responsible for N2O production and consumption in soils.
3
9
40. Molecular Techniques and stable isotope ratios at natural
abundance give complementary inferences about N2O
production pathways in an agricultural soil following a
rainfall event
40
• Snider, D., Thompson, K., Wagner-Riddle, C., Spoelstra, J., Dunfield, K. Soil Biology and Biochemistry (2015) 88, 1–17.
41. Context of Study
Sampling over a N2O emission event
•Liquid dairy manure (LDM) added to soils provides C for
denitrification and organic N and NH4-N that can be nitrified.
•Large fluxes of N2O often occur following the application of
manure to soil.
•Large N2O emissions are also common after rainfall in soils
affected by drought or extended dry periods.
42. Objective and
Research
Questions
42
• Use micrometeorological, stable isotope, and
molecular methods to determine the short-
term dynamics of N2O production processes in
soil.
• Do stable isotope and molecular
measurements provide similar inferences
about N2O soil processes occurring over an
emission event?
43. Significance of Study
This is the first field
study to combine
stable isotope and
molecular methods
to study N2O
production
processes in
manure-amended
soils in situ.
45. N-Cycling SMCs Increase
45
Significant increase in the size of the N-cycling communities
May 31 June 2 June 8 May 31 June 2 June 8 May 31 June 2 June 8 May 31 June 2 June 8
N2O
Consumption
N2O
Production
47. Microbial Results Summary
• Molecular analyses revealed abundant and
potentially active nitrifying and denitrifying microbial
communities before and after the rainfall in both fields.
• Following the onset of rain, there was a rapid
response in the soil microbial communities that
stimulated a large flux of N2O via nitrifier-denitrification
and denitrification.
48. Project Conclusions
•Stable isotopes were useful for directly tracking the
pathways of N2O production.
•Molecular analyses revealed the status of the N
cycling communities before, during and after the
emission event.
•Combined, these methods explained observed
differences in N2O fluxes between fields and gave
complementary results.
49. Project Background
• Construction of a 500
Kva DC transmission line
in 2014-2015 by ATCO in
SE Alberta provided a
novel research
opportunity to refine
BMPs for transmission
line construction.
Thompson, K., James, K., Najafi, F.,Buckley, S.,
Quideau, S.,Bent, E. Carlyle, C, and E. Bork
(5 manuscripts in prep)
50. 50
Do access mats mitigate the
negative impacts of industrial
traffic?
51. Disturbance Mitigation
Construction for oil & gas and
powerlines use modern mitigation
tools such as wooden access mats.
• Redistribute weight
• Durable work surface
• Reduce soil rutting & compression
• Prevent ripping of vegetation
• High cost & direct impacts on
vegetation
52. Study Site
• Mattheis Research Ranch –
Rangeland Research Institute,
University of Alberta
• Mixedgrass prairie
54. Soil was collected from two grassland sites (RCBD design, one
sandy and one loamy soil) in 2015 and 2016 from natural
vegetation, direct traffic, and traffic overtop of matting.
54
Direct Traffic
Access Mat+
Traffic
Natural
Vegetation
1. Extract – tells us “Who’s there?”
2. Use qPCR to quantify the number of gene ( ) copies
present – tells us “How large is the community?”
3. Use Illumina sequencing to characterize microbial
communities (diversity, community structure)
55. Traffic Treatments
Impacted Soil
Moisture
→Access mats increased soil
moisture in year 1
→Direct traffic showed
positive legacy effects on soil
moisture in year 2
→Direct traffic increased soil
compaction & bulk density,
and slowed water infiltration
SoilMoisture(g/g)
0
5
10
15
20
25
30
Control
Access Mat
Traffic Only
2015 2016
A
B
BC
CD
D
BC
58. Traffic and
Access Mats
Influenced
Total Soil
Fungal
Community
Size
2015 2016
A A
B B
→Both disturbances decreased the size of the fungal community in 2015
→ Direct traffic had positive legacy effects on the fungal community in 2016
59. Disturbance
Variably
Impacted the
Size of the
Nitrifying
Community
CON RM TON
logamoAgenecopiespergdrysoil
5.0
5.2
5.4
5.6
5.8
6.0
6.2
B
AB
A *p=0.0704
Control Access Mat DirectTraffic
→Traffic treatments influenced the size of the nitrifying community that
contributes to N O production.
60. Traffic Impacts on Fungal Communities
p<0.05
4381 bacterial 16S rRNA OTUs,
1418 ITS OTUs, and 52 archaeal
16S rRNA OTUs
Fungal community profiles were
significantly different between
AM and TON plots in both years
of sampling.
AM
CON
TON
61. Indicator Species Analysis
• 43 Bacterial OTUs
• 26 Fungal OTUs
• 6 Archaeal OTUs
CON: associated with aerobic bacterial species and C-cycling and N2-
fixing OTUs.
TON: associated with anaerobic species including Cyanobacteria spp. And
Gemmata spp.
AM: associated with a number of potential fungal plant pathogens
62. Conclusions
AM placed on actively growing vegetation for
12 weeks in the spring had a large impact on
soil microbial communities, particularly fungi.
The use of AM should not be undertaken
without consideration of soil texture and
amount of traffic prairie will be exposed to.
AM did not sufficiently mitigate impacts of
industrial traffic on soil microbial communities
– however, this study utilized a limited number
of traffic passes.
64. Project Summary
Fungal communities and some N-cycling
microbial groups responded to the type of
traffic disturbance and tower construction
methods, suggesting different construction
techniques may alter soil C storage, and the
potential of the microbial community to
produce and consume N2O, therefore
influencing associated ecosystem
functioning during grassland recovery.
65. Current Work Underway is Addressing the Role of AMP
(adaptive, multi-paddock) Grazing on soil C, microbial
communities, plant communities, and GHGs
65
66. Summary
• Soil microbial communities are
influenced by our
management choices
• Interdisciplinary, systems-
based approaches are required
• Successful production relies on
management of soil microbial
communities that promote
crop productivity and efficient
input use
67. Future Research
Linking changes in soil microbial
communities with agricultural management
within specific:
•Climates
•Geographies
•Soil types
•To determine the fate of C and N in soil
•To create BMPs to decrease N losses, build
soil C, maintain or promote EGS from our
agro-ecosystems.
67
