Soil Microbiology and Its Effects on

Nutrient Availability and Uptake in

Plants (and other things)

Kate Scow
kmscow@ucdavis.edu
Dept. of Land, Air & Water
Resources
Agricultural Sustainability Institute

Outline
Soil biodiversity and farming (short film)
Role of soil microbes in growing things
Organic matter
Nitrogen cycling
Phosphorus cycling
Soil structure

Managing soil biology for plant growth and

sustainability
Indicatorshow do we measure how we are doing?
Discussion

Film

Above ground diversity is often intentionally low in managed systems

Most ecoecosystems concentrate

biodiversity belowground

Soil is one of most diverse microbial habitats: Thousands of species

can be detected in gram of soil. Most not yet iden>ed nor their
func>on(s) known.

Microbes include: Bacteria, Archaea, and Fungi. Of bacteria and
Types
of soiltaxa
organisms
archaea, ~1500
dierent
detected in CA cropping systems.
centipede
rove
beetle

pseudo scorpion

ant
flatworm
ground
beetle

mite

adult fly

fly
larvae

roundworms
beetle

mite

rove
beetle

bacteria

millipede

fungi

archaea archaea

snail

mite

And archaea and fungi

earthworm
organic debris

diagram berdasarkan konsep Dr. Daniel Dindal, 1978

Breakdown
wastes, make
compost

Remove pesticides and

nutrients in buffer strips

Build soil
structure

Contribute to

biodiversity

http://images.google.com/imgres?imgurl=http://www.sare.org/
publications/explore/images/scenewide2.jpg

Develop antibiotic
resistence (or not)

Support plant and

animals via

mutualism

Contaminate
food (or not)

Sequester

carbon

Biodegrade

pesticides in
field

Source/sink

of GHG

Build soil
organic matter

Control and cycle
plant nutrients

Fix nitrogen

Support farmers
digestion and immunity

Fight/suppress

pests (IPM)

How microorganisms contribute to farms and gardens (the good, the bad
and the ugly)

Microbes tightly coupled with plants and soil: cant decouple biodiversity from soil
Climate

Management

Water/

Nutrient

Supply

Drivers

Crop rotation

Organic Resource Quality

Tillage

Factors
Synchrony

Water/Nutrient Use

Processes

Plant and
Soil
Biodiversity

Soil Properties
and processes

Carbon
and
Nutrient
Cycles

Maintaining

soil

structure

Nutrient Use Efficiency

e.g., Organic
matter, texture

Water Use Efficiency

Services
Carbon Sequestration

Sustainable
Agroecosystems

Adapted from
Brussaard et al. 2007

Climate
BUILDING

ORGANIC MATTER

Management
Crop rotation

Organic Resource Quality

Tillage

Plant and Soil

Biodiversity

Carbon
and
Nutrient
Cycles

Soil Properties
and processes

Maintaining

soil

structure

Nutrient Use Efficiency

Water Use Efficiency

Carbon Sequestration

e.g., Organic
matter, texture

Soil organic matter (SOM) formation

Microbes are enzymatic drivers and also feedstock for SOM

Persistence of soil organic matter as an ecosystem property (2011) Schmidt et al. Nature 478, 4956

Health & Medicine

Mind & Brain

Plants & Animals

Earth & Climate

Space & Time

Matter & Ene

search (UFZ), the Technische

... from universities, journals, and other research organizations
Science News
n (Technical University of
Fertile Soil Doesn't Fall from the Sky: Contribution of Bacterial
versity of Stockholm, the Max-
Remnants to Soil Fertility Has Been Underestimated Until Now
Entwicklungsbiologie (Max
Dec. 14, 2012 Remains of dead bacteria have
enlarge
Developmental Biology) and the
far greater meaning for soils than previously
assumed. Around 40 per cent of the microbial
t Hannover (Leibniz University
biomass is converted to organic soil components,
ournal Biogeochemistry.
write researchers from the Helmholtz Centre for

Just
Olde

Soc

Reco
and

Environmental Research (UFZ), the Technische

Universitt Dresden (Technical University of
Until now, it was assumed that the
Dresden) , the University of Stockholm, the Max-
organic components of the soil were
Planck-Institut fr Entwicklungsbiologie (Max
composed mostly of decomposed
Planck Institute for Developmental Biology) and the
plant material which is directly
Leibniz-Universitt Hannover (Leibniz University
Hannover) in the journal Biogeochemistry.
converted to humic substances. In a

The electron micrograph shows bact

Othe
(Hyphomicrobium sp;. Yellow) growin
Sh
solid surfaces, floors and sediment g
growth whatsoever cells die and defo
Until now, it was assumed that the fragmenting cell envelopes remain. S
laboratory experiment and in field
Bre
organic components of the soil were The electron micrograph shows bacteria
Share This:
fragments of these shells (red) then
(Hyphomicrobium sp;. Yellow) growing up partly on
composed mostly of decomposed
testing the researchers have now
Ind
Like 218
solid surfaces, floors and sediment grains. During
plant material which is directly
microparticulate matrix in soils and s
refuted this thesis. Evidently the
mi
converted to humic substances. In a growth whatsoever cells die and deformed or
ye
fragmenting cell envelopes remain. Small-scale
Tweet 42
laboratory experiment and in field
(Credit: Burkhard Schmidt-Brcken,
easily biologically degradable plant
fragments of these shells (red) then set the
testing the researchers have now
"V
Material science/TU Dresden; Colore
microparticulate matrix in soils and sediments.
6
material is initially converted to
refuted this thesis. Evidently the
lea
(Credit: Burkhard Schmidt-Brcken, Institute of
easily biologically degradable plant
Pl
Schurig/ UFZ)
microbial biomass which then
Material science/TU Dresden; Colored by Christian
72
material is initially converted to
NA
Miltner
et al.. SOM genesis: microbial biomass as a
Schurig/ UFZ)
microbial biomass which then
Persistence
of soil organic matter as an ecosystem property
(2011) Schmidt et al. Nature 478, 4956

provides the source material to soil
po
significant source. Biogeochemistry, 2011

provides the source material to soil
Mi


organic matter.
organic matter.
See Also:
Soil organic matter represent the

Related Stories
Related Stories

Su

Microbial Biomass

Soil organic matter link to microbial biomass

Soil organic carbon

1.4%
1.0%

0.78%

Carbon/nitrogen ratio

9.4
10.2

11.5

tomato

wheat

tomato

If soil organic ma.er contains higher propor3on of microbial

biomass carbon, is it be.er nutrient source?

Microbial biomass is early indicator of changes in total soil organic

carbon.



Microbial biomass is indicator of how much N available to plant
over season from organic matter in soil.

Microbial biomass nitrogen and release of nitrogen

decreasing with depth (Murphy et al., 1998).

Soil Quality WebsiteWest Australia http://soilquality.org.au/factsheets/making-sense-of-biological-indicators

Climate
NUTRIENT
CYCLING: N and P

Management
Crop rotation

Organic Resource Quality

Tillage

Plant and Soil

Biodiversity

Carbon
and
Nutrient
Cycles

Soil Properties
and processes

Maintaining

soil

structure

Nutrient Use Efficiency

Water Use Efficiency

Carbon Sequestration

e.g., Organic
matter, texture

NUTRIENT CYCLING
Managing the N cycle means managing
microbes
Plant N use efficiency often low, <50% of N added is
taken up into plants immediately
Uptake is regulated by relationships between soil
microorganisms and plants. Large amount of fertilizer,
NOT MATTER THE FORM, goes through microbes
before plant gets it.

Managing the N cycle means managing microbes

(diagram from Jackson et al., 2008 (Ann Rev Plant Biol 59))

Shaded circles show microbial processes or inuences

Mineral
P taken up

and
PHOSPHORUS???

in soil solution; general
microbial activity
increase P availability.
Mycorrhizae help find
and take up.

Organic P relies on
decomposition of
organic material to be
released

CREATING/MAINTAINING

Climate
SOIL

STRUCTURE

Management
Crop rotation

Organic Resource Quality

Tillage

Plant and Soil

Biodiversity

Carbon
and
Nutrient
Cycles

Soil Properties
and processes

Maintaining

soil

structure

Nutrient Use Efficiency

Water Use Efficiency

Carbon Sequestration

e.g., Organic
matter, texture

SOIL STRUCTURE
Role of organic matter and microbes in creating
structure: fueled by carbon inputs

Implications of structure for water movement and gas exchange

Management practices for managing microbes in soil

Manipulate what they eat: C/N ratio of organics, degradability, physical
availability, electron acceptors (e.g. oxygen), other nutrients, specific enzyme
co-factors (?)
Other soil amendments: biochar, calcium, signaling compounds?
Manipulate their environment: water and oxygen content, pH, architecture.
Less harsh chemicals. Less physical disturbance. Minimize periods of no cover.
Inhibit/select for specific microbial groups? Nitrification inhibitors? Or through
substrates?
Promote symbiotic relationships with plants that short-circuit some of the soil
processes providing Nless physical disturbance for mycorrhizal fungi?
Inoculate with consortia, specific strains?.often equated with soil biology
but evidence for efficacy is inconsistent. Lot to learn.

Indicators: what do we measure to show how we are doing?

Indicators, metrics for soil biodiversity

Indicator

How measure

Why useful

Who are they and who is in their

communities? How diverse are
they?

Sequencing of 16/18S rRNA:

probing or PCR, including clone
libraries, pyrosequencing, DNA
fingerprinting, metagenomics

Determines WHO is there based on

universal phylogenetic standard,
helps understand evolutionary
relationships, gives idea of
potential

How many/much are they?

Numbers
Biomass

Fumigation-extraction, PLFA, DNA,

microscopic counts, quantitative
PCR

Estimates amount of nutrients in

microbial biomass. Gives an idea of
how fast they carry out functions.

What functions do they perform?

Degrades chemicals, produces
chemicals
Associates with a symbiont
Kills someone
Competes with someone
Functions within some niche
Helps build soil structure

Substrate utilization, product

formation (respirometry, GC, GCMS, measure stable isotopes--natural
abundance, labeled compounds).

Measures the actual impacts of

microorganisms on environment
through what they remove, release,
etc.

How are they doing?

Viability
Stress markers

ATP charge, PLFA stress markers,

vital stains, RNA expression

Presence/quantity of functional
genes (Geochip, PCR or probing);
RNA expression of functional genes

Measures the potential and or

activity of genes responsible for
specific microbial processes
Are organisms metabolically active?
At full capacity? Are they stressed??

Challenges and benefits in managing soil biology rather

than relying only on chemically based systems
Much of what we think of as soil processes is actually
biological activity.
Indirect management practices often more fruitful than direct
manipulation of biology
Everything is connected
Challenging because cant isolate specific factors
Good in that can manage for multiple benefits
Important to evaluate trade-offs and identify indicators

Challenges and benefits in managing soil biology rather

than relying only on chemically based systems (2)
Takes time to invest in system w/eye on future (not this growing
season) to get it to where the positive benefits are substantial and
consistent.
Resistance/resilience of agroecosystems is largely due to
biological systems
May not have quick fixes to problems (e.g., chemicals in organic
or more biological system)so need to design resilience into
systemour expanding knowledge of microbial communities
well help

Helpful tools and resources

Oregon State University Organic Fertilizer and Cover Crop
Calculator http://smallfarms.oregonstate.edu/calculator
NRCS Soil Health Initiative
http://www.nrcs.usda.gov/wps/portal/nrcs/main/soils/health/

Cornell University Soil Health Initiative http://soilhealth.cals.cornell.edu/

Soils are Alive online textbook (Australian Soil Club)
http://www.soilhealth.com/soils-are-alive/

Sustainable Soil Management (Appropriate Technology Transfer

for Rural Areas
http://www.soilandhealth.org/01aglibrary/010117attrasoilmanual/010117attra.html

Film: Symphony of the Soil http://www.symphonyofthesoil.com/