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Harnessing (roots and) soil biology
John KirkegaardCSIRO Plant Industry
What is “soil biology”?
Conservation farming - principles
● Minimum mechanical soil disturbance
● Permanent soil cover (crop or mulch)
● Diverse crop and pasture species
Improving productivity of modern, no-till farming
Adoption is driven by
● Erosion control, water conservation
● Labour, machinery, fuel savings
● Timeliness of operations
● Soil “health” benefits
● Improved productivity
Llewellyn et al, (2012) Field Crops Research 132, 204-212
Farming systems
Disturbed soil
UnderstandingLaboratory Undisturbed soil
The new environment for roots to perform
500 m
rhizosphere
Wheat rootRoot hair
Image with cryo-scanning microscope, Watt et al., 2005
Long-term study at Harden (25 years)
Improvements in soil parameters Good establishment Poor early vigour and yield
No-till/Retain vs Cultivate/Burn Wheat-Break crop 30 m x 6 m (4 replicates)
Growing season rainfall (mm)
0 100 200 300 400 500 600
Yiel
d di
ff (R
DD
-BC
) (t/h
a)
-1.5
-1.0
-0.5
0.0
0.5
1.0Yield gain
Yield loss
HARDEN
WAGGA
Kirkegaard (1995), (unpublished)
4 8 12 16 20 24
Improving productivity in no-till
Strategies to improve productivity in intensive cereal systemsWhy do some varieties perform better?
Reducing impact of Rhizoctonia in no-till systemsUnderstanding biological suppression in soil
Investigating compatibility of livestock in no-till systemsImpacts of sheep on soil and water use
Improving organic-matter build-up in stubble retentionLimit may be nutrients rather than carbon input
Clive Kirkby
Hunt, Kirkegaard, Bell
Michelle Watt
VVSR Gupta
Poor early vigour - biological constraints
No-till Cultivate No-tillFumigate
(Kirkegaard et al, 1997; Simpfendorfer et al, 2002)
Intact soil cores from field
0
4
8
12
Cultivated No-till
Pseudomonasper mm root (x 103)
Cultivated soilFast growing roots
No- till soilSlow growing roots
Inhibitory bacteria on root tips in no-till soil
(Watt et al 2005, 2006)
Options to improve crop vigour in no-till
Encourage rapid root growth
Sow early into warm soil
Disturb the soil below the seed using deep points
Select vigorous variety (Watt et al 2005)
Strategic tillage – makes good sense
< 5% practice multiple cultivation pre-sowing
No-till adopters use cultivation on 30% area
88% use narrow points only (rather than discs)
Discs used to sow ~30% cropped area
GRDC 2010; Llewellyn et al 2012
Farmers adopt flexible approach to no-till
Occasional tillage - irreparable soil damage..?
Case specific, but evidence is contested
Strategic tillage can resolve some issuesweed, disease management, lime incorporation (23M ha acid soils)
Recent study completed at Harden (Bissett et al, 2012)
microbial biomass, community structure, diversity and function(rDNA & rRNA, TRFLP)
diversity shifts across cropping cycle and treatments
little evidence of long term effects on biomass or function
Soil carbon changes slow or absent
Rumpel (2008) no change after 31 years
Luo (2010) no difference in C at 69 paired sites
Stubble retention - the carbon “conundrum”.....
Rumpel et al (2008) J. Soil Sci. Pl. Nutr. 8, 44-51;
Luo et al (2010) Agric. Eco. Envir. 139, 224-31
What’s going on.....?
Living(up to 10%)
Light Fraction(dead but active)
(up to 20%)
Soil Organic Matteror humus
(very dead)(up to 95%)
Soil Organic Material – where is the C?
Its soil organic matter NOT carbon....
Target is stable organic matter (humus) NOT soil carbon
Stable organic matter has a constant ratio of C:N:P:S
Like bricks (C) and mortar (NPS) to build a stable brick wall
Nutrients (not C) might limit humus formation from residues
Dr Clive Kirkby PhD
Stable organic matter has constant CNPS ratio
Total soil N (%)0.0 0.2 0.4 0.6 0.8 1.0 1.2
Tota
l soi
l C (%
)
0
2
4
6
8
10
12
14
16761 soils from various countries105 Australian soils collected from four of the five mainland states
r2=0.93
Total soil S (%)0.05 0.10 0.15 0.20
531 soils from various countries105 Australian soils collected from four of the five mainland states
r2=0.85
0
C:N C:S
500+ international and 100+ Australian soils
1000 lbs C requires 92 lbs N, 18 lbs P, 14 lbs S
Kirkby et al (2011) Geoderma 162, 197-208
Nutrients increase C-sequestration from residue
Kirkby et al (2012)
Leeton
Incubation cycle0 1 2 3 4 5 6 7
Car
bon
(%)
1.5
2.0
2.5
3.0Soil + stubble + supplementary nutrientsSoil + stubble
error bars are SE
Repeated addition of 5 t/acre wheat straw (3 monthly)
Hum
us c
arbo
n %
5 t/acre wheat straw+ nutrients NPS
5 t/acre wheat straw
Laboratory incubation study (Harden soil)
(7 x 3-month cycles)
Losing “old” soil C while making “new” carbon
Harden
Cha
ne in
car
bon
(mg
kg s
oil -1
)
-2000
0
2000
4000
6000
error bars are SE
+4
-29
-7% -7
+33%
+46%
-15
+31
new C gainedold C lostnet change
soil + straw soil + straw+ nutrients
soil alone(control)
5 t/acre equivalent C13-labelled straw added – single cycle
Kirkby et al (2012)
Soil only Soil + Straw Soil + Straw+ Nutrients NPS
Buntine sand + stubble incubation (5 weeks)
Clive Kirkby (PhD)
It works in the field – Harden field site
We mulch the stubble then
Add granular fertiliser to one plot
No fertiliser on adjoining plot
+ _
Incorporate stubble
+ _
Humus-C increase of 7.5 t/ha after 3 years to 1.6 m
Carbon (t/ha)0 2 4 6 8 10 12
Dep
th (1
0 cm
incr
emen
ts)
123456789
10111213141516
stubble + nutrientsstubble
total C t/ha56.549.0
52% of C is below 30 cm
Nutrient Amount (kg)
Approx price/kg nutrient Approx Cost ($)
N 92 1.50 138P 18 3.50 63S 14 1.00 14
$215
Implication – hidden cost of C-sequestration
Every 1 tonne of C-sequestered
requires
Australian government currently values CO2 at ~$23 / tonnethis equates to $84 per tonne of C
Implications of nutrient ratios to build SOM....
C sequestration limited by nutrients, not C in no-till systems
Nutrient management in no-till (spray onto residue?)
Is strategic tillage necessary to sequester C from residues?
Nutrient-use efficiency vs C-sequestration?
Implications for:
manures, cover-crops, biochar, municipal wastes etc.....
Crop and pasture sequence
20 - 25 kg of shoot N fixed per tonne of legume biomass produced
at least 40% of N in cereals derives directly from previous legume N
high input of labile C and N in plant and organic animal residues
pasture increases organic carbon (~ 0.15% per year for 5 year)
improves soil structure (aggregate stability increase 5 -10%/yr)
Important biological impacts of legume-based pastures
Broadleaf rotation crops (legumes, canola)
Disease control(root and stubble borne)
Weeds(control of grass weeds)
NitrogenLegumes (+20 to 50 kg/ha N)
Residues easy to retain
20% (0.5 t/ha) yield benefit
Water and nutrient efficiency
Kirkegaard et al (2008) Field Crops ResearchSeymour et al (2012) Crop and Pasture Science
Root exudates, soil biology and crop growth
HUP- legumesH2 released into soil
(1500 gallons/ha/day)
Citrate release
White lupins
Brassicas
Isothiocyanates
Growth-promoting bacteria
(Peoples et al, 2008)
Improves P availability
(Hocking 2001)
Pathogen suppression
(Kirkegaard et al, 2008 )
Not all break crops are equal
Previous cropWheat Oats Linseed Canola Mustard
Yie
ld (
t/ha
)
3.00
3.25
3.50
3.75
4.00
Kirkegaard et al (2008) Field Crops Research
GFP-labelled fungus
Biofumigation – isothiocyanates from canola roots
glucosinolates Myrosinaseenzyme
Isothiocyanates(ITCs)
2 cmInside canola root
Dale Gies, Moses Lake – potato disease control
Diseases managed
Verticillium wiltSclerotiniaRhizoctonia
StreptomycesNematodes
Mustard green manure replaced Metham sodium
√ Yield/quality maintained√ $US 169/ha saving√ Wind erosion control√ Increased water infiltration√ Improved soil organic matter√ CO2 saving 2t C/ha/yr (1.0 mill km by plane)
Andy McGuire WSU (2004); Dale Gies (2004)
USA – Pacific Northwest
35,000 ha green manure mustard
But...intensive cereals dominate (64 to 80%)
Why cereals?easy to manage, market - low riskmore residues for cover/grazing
New technology helpsdisease resistance, soil/seed fungicides, soil DNA testingnew precision inter-row sowing, herbicide options
Yield penalties persist (5-10%)in absence of obvious disease, N or other known factorsevidence for bacterial involvementworth $200M pa
5 mm
Live wheat crop roots
Dead roots frompreceding crop
Pore in no-till soil
(Watt et al., 2005; ME McCully, images)
No-till root environment....not all good!
Hard soil – no roots
CarbonSugarsPhenolicsAcidsSignals
Last year’s dead roots Current roots
Microbial succession on old and new roots
Watt et al (2005)Cryo-scanning EMcourtesy: Margaret McCully
Actinomycetes
Janz H45 Vig18TriticaleOats Janz H45 Vig18TriticaleOats Janz H45 Vig18TriticaleOats2006cereal
0
20
40
60
80
100
120
140
160
Janz Janz Janz Janz Janz H45 H45 H45 H45 H45 Vig18 Vig18 Vig18 Vig18 Vig18
Shoo
t dry
wei
ght i
ncre
ase
(% J
anz
on J
anz)
2007 wheatJanzH45V18
2007
Can rotating wheat varieties help?
Intact core studies
Recent study on bacterial succession
Two-year wheat-wheat field study
Plating, T-RFLP, Pyrosequencing
Time (2 seasons)Variety (2)Soil type (2)Position (rhizoplane, rhizosphere, soil)
Outcomes Donn et al, 2012 (in preparation)
Position (space) and root age (time) significant determinants of populations
Season, soil type, previous crop, current genotype minor determinants
Inconsistent effects on growth and yield
5 mm
Year 1 wheat Year 2 heat
Dead wheat root
Mixture young anddead roots
Young wheat root
0.01 mm
Bacteria labelled with DNA probes
Changes in microbe populations across sequence
0
20
40
60
80
100
0
20
40
60
80
100
0
20
40
60
80
100
0
20
40
60
80
100
0
20
40
60
80
100
0
20
40
60
80
100
γ δ β α
Rhizobiaceae Caulobacteraceae BradyrhizobiaceaeSphingomonadaceae unclassif ied α-proteo incertae sedisPhyllobacteriaceae Hyphomicrobiaceae AcetobacteraceaeOther
Oxalobacteraceae Burkholderiales incertae sedisBurkholderiaceae Comamonadaceaeunclassif ied NeisseriaceaeOther
Pseudomonadaceae Xanthomonadaceae γ_unclass
Enterobacteriaceae Sinobacteraceae Other
Streptomycetaceae Microbacteriaceae unclassif iedMicromonosporaceae Kineosporiaceae NocardioidaceaePseudonocardiaceae Geodermatophilaceae Mycobacteriaceaeunclassif ied Micrococcaceae Other
FlavobacteriaceaeSphingobacteria_unclassCytophagaceaeCryomorphaceaeOther
SphingobacteriaceaeChitinophagaceaeunclassif iedBacteroidetes_incertae_sedis
Bacteroidetes
Proteobacteria
ActinobacteriaTB LB
Alpha-proteobacteria
Beta-proteobacteria
Gamma-proteobacteria
TB LB
%
Change in community composition with time and root compartment
OrderClassPhylum
Rhizoplane Rhizosphere(TB) (LB)
Assessment of the wheat root soil microbiome
unclassified Bacteroidetes Acidobacteria
Chloroflexi TM7 Firmicutes
Proteobacteria Actinobacteria other
0
20
40
60
80
100
gp
V1 R1 Sb V2 V1 R1 V2
year1 year2
The Challenge – How does community succession influence crop performance?
‐ nutrient availability‐ growth promotion‐ disease suppression
Can the microbiome be managed for agronomic benefit?
3
-
-
“Not everything that is important can be measured,
and not everything that can be measured is important...”
Albert Einstien
Soil biology and health.........
Roots for the future.....weed suppressive?
Wasson et al (2012) J. Exp. Bot. 63, 3325-33
Sorgoleone onsorghum root tips
New frontier - root-soil biology research
● Synergies from …
new root genetics
precision placement
novel input/formulations
Understanding
Farming systems
Lab Tilled No-till
Further gains in efficiency and productivity
Thank youCSIRO Plant IndustryJohn Kirkegaard
Email: [email protected]
Contact UsPhone: 1300 363 400 or +61 3 9545 2176Email: [email protected] Web: www.csiro.au
Many colleagues, farmers and friends.....