How Soil Microbes Transform Plant Residues into Soil ...

How Soil Microbes Transform

Plant Residues into Soil Organic

Matter to Maintain Healthy Soils

Dr. Bobbi Helgason

Associate Professor, Soil ScienceUniversity of Saskatchewan

Alberta Institute of Agrologists Helgason Webinar Dec 3, 2020

Where does soil organic matter

come from?

https://theconversation.com/soil-carbon-is-a-valuable-resource-but-all-

soil-carbon-is-not-created-equal-129175

In agroecosystems most

new organic carbon

comes from plants (and

organic amendments).

Energy held by plant

carbon fuels other

important processes

(e.g. nitrogen cycling).

Graphic: J. LavalleeAlberta Institute of Agrologists Helgason Webinar Dec 3, 2020

https://theconversation.com/soil-carbon-is-a-valuable-resource-but-all-soil-carbon-is-not-created-equal-129175

Why do microbes matter for SOM?


“Soil C sequestration is a ‘win–win’ option, a ‘no-regrets’ option, because a soil with more organic C, we say, is a better soil, a more productive soil”…“But now we encounter a disquieting constraint—the benefits of organic matter arise, not from its accumulation, but from its decay.”

Henry Janzen, AAFC Lethbridge

How does plant organic matter

become soil organic matter?

ODE TO ROT (J. Updike 1985)

“ ‘Let there be rot’, and hence bacteria and fungi sprang into existence to dissolve the knot of

carbohydrates photosynthesis achieves in plants, in living plants…

…Dead matter else would hold the elements in thrall -- nitrogen, phosphorus...” Alberta Institute of Agrologists Helgason Webinar Dec 3, 2020

Microbial decomposition

Soil organic matter supports biota

Increased microbial

abundance and diversity

Improved soil

functioning

=

healthy soil!

Microbial Abundance = capacity

Microbial diversity = insurance


Soil biota: ecosystem services

Decompose & cycle organic matter

Regulate nutrient availability

Suppress pests and disease

Maintain soil structure & hydrology

Exchange gas and store carbon

Detoxify soil

Control plant growth

The new paradigm of SOM formation


Emerging view of soil

organic matter:

• Microbial accessibility

• Focus on C flows rather

than stocks

…a changing paradigm

The contentious nature of soil organic matterLehmann and Kleber, 2015 Nature

What affects SOM loss?

3 SOM destabilizing factors:

1) Desorption from minerals• Soil pH, increased moisture

2) Release from aggregates• Tillage, freeze-thaw, wet-dry cycles,

bioturbation

3) Increased biotic metabolism• Quality of litter, quality of soil

organic matter, microbial carbon use efficiency

Bailey, et al. 2019. Env. Res. Lett. 14: 020034


The contentious nature of soil organic matterLehmann and Kleber, 2015 Nature

Organic matter supports healthy soils

https://www.quartoknows.com/blog/quartohomes/2015/04/22/sustainable-gardens-and-organic-matter/


Practices that can build SOM

Continuous cropping

Reduced physical disturbance

Diverse cropping rotations

Balanced nutrient management

Organic amendment application

Cover cropping

Not all soil organic matter is created

equally

https://www.freepik.com/premium-photo/fertile-loam-soil-suitable-

planting-soil-texture_4882973.htm

https://theconversation.com/soil-carbon-is-a-valuable-

resource-but-all-soil-carbon-is-not-created-equal-129175Alberta Institute of Agrologists Helgason Webinar Dec 3, 2020


https://theconversation.com/soil-carbon-is-a-valuable-resource-but-all-soil-carbon-is-not-

created-equal-129175

Particulate organic matter

(POM):

• protected within

aggregates

Mineral-associated organic

matter (MAOM):

• protected by binding with

clay minerals


Not all soil organic matter is created

equally


Tools for tracing carbon in soil and

microorganisms13C tracer: stable isotope of carbon with 6 protons and 7 neutrons

https://deskarati.com/wp-content/uploads/2015/07/Carbon-Isotopes.jpg

DNAPhospholipid fatty acid (PLFA)


https://deskarati.com/wp-content/uploads/2015/07/Carbon-Isotopes.jpg

Tillage as a destabilizing factor

Fall 2007, microcosms set up (Lethbridge + Ottawa)

Barley residue (13C at ca. 10 atom %) added either:

a. incorporated (0-10cm)

b. surface applied

(unlabeled residues every fall)

mixed residue surface applied residue

Collaborators: Drs. Henry Janzen, Ben Ellert and Ed GregorichAlberta Institute of Agrologists Helgason Webinar Dec 3, 2020

https://deskarati.com/wp-

content/uploads/2015/07/Carbon-Isotopes.jpg


2 years after 13C barley residue added

Lethbridge (drier, cooler):• Less residue remains when

incorporated

Ottawa (wetter, warmer): • residue decomposes faster

• decomposition is less affected

by residue incorporation

Alberta Institute of Agrologists Helgason Webinar Dec 3, 2020Helgason et al. 2014 Soil Biology and Biochemistry


“Ordination” visualizes differences between complex communities

LethbridgeOttawa

Different microbes are active in NT vs. CT.

Helgason et al. 2014 Soil Biology and Biochemistry

*ordination

Changes in organic matter composition? Alberta Institute of Agrologists Helgason Webinar Dec 3, 2020

Residue type affects decomposition

Why does canola residue produce higher than expected

soil N2O emissions?


Akeem Shorunke, MSc(Rich Farrell co-supervisor)

Soil microbes prefer canola residue


Canola residues are particularly tasty; drives a microbial feeding frenzy

O2 gets consumed so microbes use NO3- instead (i.e. denitrification)

Most of the N2O-N came from the soil (not the residues) “priming”


Each residue type formed a different

community structure

Microbial community structure

What is the net effect on

soil organic matter

formation?



N2O emissions

How does crop diversity affect SOM?

Tiemann et al. 2015 Ecology LettersAlberta Institute of Agrologists Helgason Webinar Dec 3, 2020

How does crop diversity affect SOM?Long-term cereal monoculture vs. diverse rotations

AAFC New Rotation Experiment (Swift Current est. 1987)

continuous wheat vs. wheat-canola-wheat-pea (n=3)

AAFC Totten Rotation Experiment (Harrow est. 2001)

continuous corn vs. corn-soybean-winter wheat (n=4)

www.winnipegfreepress.com

Dr. Jennifer TownAAFC, Saskatoon RDC

AAFC collaborators E. Gregorich, C. Drury, R.

Lemke, L. Phillips


How does crop diversity affect

microbial communities?

Location Stage Date

Harrow, ON Early Vegetative (EV) June 21 Anthesis (AN) August 3 Post-harvest (PH) December 5 Swift Current, SK Early Vegetative June 6 Anthesis July 20 Post-harvest September 12

Biogeochemistry

PO4, NO3, total N,

total and organic

C

Microbial enzyme

activities

Organic Matter

Characterization

Lignin (lignin phenols)

Amino sugars

Available C (CO2

respiration; 38d)

Microbial community

characterization

DNA sequencing

Phospholipid fatty acids



Wheat: little difference in soil microbial community

structure and diversity


Bacteria

Fungi


Diversity

bacteria fungi

Seasonal progression

Community structure

Corn: soil microbial community structure differed

(diversity did not)


Bacteria

Fungi

Diversity

bacteria fungi

Seasonal progression


Community structure

Diverse crop rotations resulted in

different soil functioning



Crop rotation affected SOM quality



Diverse crop rotations resulted in

different soil function

Aboveground diversity

Belowground diversity function

interact to improve

fertility and soil organic

matter

Crop rotation affected nutrient

cycling, microbial community

structure and SOM composition

corn > wheat

Plant matter quality is important for fertility Alberta Institute of Agrologists Helgason Webinar Dec 3, 2020


Organic matter: what about roots?

upload.wikimedia.org/wikipedia/commons/a/a7/4_Seasons_Roots.jpg

Roots can contribute up to 80% as much C as aboveground biomass (Fan et al. 2019)


What is the big deal with roots?

Rhizodeposition can account for up to 30%

of net photosynthate C

Philippot et al. 2013. Nat Rev Microbiol 11:789-799

https://doi.org/10.1371/journal.pbio.2006352.g002


Emerging evidence that root C is preferentially stabilized(e.g. Sokal et al., 2019)

Intercropping, cover cropping

Organic matter: what about roots?

How does microbial stabilization of

root carbon change with depth in the

soil profile?

The role of functional traits of wheat,

canola and lentil roots on microbial soil

C and N cycling in the rhizosphere


Mostafa Hojati

Kehinde Adams (aka “Adams”)

Organic matter supports healthy soils


Soil organic matter provides

resilience to stress

Photo: Soil Sc ience Society of America ACSESS Digital Library

Soil management practice

Reduced physical disturbance

Continuous cropping

Diverse cropping rotations

Cover cropping

Balanced nutrient management

Organic amendment application

A big thanks to my talented team!


Acknowledgements


Thank you!


[email protected]

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