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Kirkegaard (1995), (unpublished)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: john.kirkegaard@csiro.au

Contact UsPhone: 1300 363 400 or +61 3 9545 2176Email: Enquiries@csiro.au Web: www.csiro.au

Many colleagues, farmers and friends.....