management of soil biota - welcome | field crops of the soil biota •plant pathogens & disease...

Management of Soil BiotaPathogens, Diversity, Key Symbioses

Importance of the Soil Biota

Interactions with Physical Environment

• Nutrient Cyclingand Storage

• Aggregation and Aggregate Stabilization

• Biomass Contribution to Organic Matter

• Residue Incorporation and Breakdown

Interactions with Plant Community

• Nutrient Access

• Plant Growth Promotion

• Plant Establishment

• Plant Disease

• Plant Disease Suppression

Ecosystem services: Water purification, Toxin breakdown, C sequestration

Plant Disease: Soil-Borne Pathogens

• Fungal: e.g. Rhizoctonia, Verticillium

• Bacterial: e.g. Streptomyces, Ralstonia, • Residue-borne issues such as Clavibacter michiganensis

sub nebraskensis or Erwinia chrysanthemi pv. zeae

• Oomycetes: Pythium, Phytophthora,

• Viruses: • SBWMV (vector: protozoan), • Tomato Black Ring Virus, Grapevine Fanleaf Virus

(vectors: nematodes)

• Nematodes: Meloidogyne, Heterodera

Management of the Soil Biota

• Plant Pathogens & Disease• Management Considerations

in Relation to Soil Health

• General Principles for Managing Soil Biological Health

• Plant and Soil Biodiversity

• Key Manageable Symbioses

Host

Pathogen Environment

Disease

Host


Disease

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et.o

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Host


Disease

www.apsnet.orgwww.uoguelph.ca/~gbarron

Host


Disease

Fusarium Head Blight Disease Cycle

Fusarium head blight - Disease Cycle (Courtesy A. Schilder and G. Bergstrom) apsnet.org

Fusarium head blight in wheat. (Photo: G. Bergstrom)

Phytophtora Root and Stem Rot

Phytophthora sojae

Soybean Cyst Nematode

Photos from apsnet.org

Managing Disease Epidemics

Host


Disease

Dis

ease

Time

Disease Progress Curve


Dis

ease

Time



Dis

ease

Time


HOW?

Management Strategies

Target the pathogen:

• Fungicides, nematicides, fumigants

• Some quite effective

Systemics, cf. Protectants

• Risk of non-target effects

Host


Disease







A complex food web is needed for releasing mineral nutrients







• Sometimes High Toxicity

• Environmental Impact

• Blank Slate Effect

(Blank Slate = Blank Check)



• Biocides

• Overwintering Structures• Tillage to incorporate residue



• Biocides

• Inoculum Source

• Sanitation!

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• Biocides


• Subsoil compaction

• Saturated conditions

• Stressed roots

Host


Disease



• Biocides


May create conducive environment

• Subsoil compaction

• Saturated conditions

• Stressed roots


Improve Soil Environment:• Reduce disease-conducive conditions

• Improve drainage• Many pathogens exacerbated by wet and

waterlogged conditions

• Decrease / Avoid compaction• Improves drainage and decreases root

stress

• Residue / Mulch / Soil Cover• Decrease lower-canopy humidity

Host


Disease


Manage the Host

• ResistanceHost


Disease

Strategies for Disease Control

• Resistance: host plant genetics reduce susceptibility

• Exclusion: prevent pathogen from coming in contact with plants

• Protection: chemical or physical barriers between plant and pathogen; environmental manipulation to favor plant growth, disfavor pathogen

• Eradication: eliminate pathogen inoculum directly at its source

• Avoidance: planting in time or space to avoid pathogens and/or conducive environments

• Therapy: treat individual diseased plants to reduce or eliminate pathogen

Plant Resistant Varieties

Two wheat varieties showing differing levels of Fusarium head blight. (apsnet.org)

Partial resistance to Phytophthora sojaemeasured in a layer cup test. (apsnet.org)


Manage the Host

• Resistance

• Diversity of Hosts• Spatially

Host


Disease

Cultivar Mixtures: Barley in Germany

Dilution and Barrier Effects


Manage the Host

• Resistance


• Temporally• Rotation

• Cover Cropping

Host


Disease

per 40 ft of row Root Rot

Severity

Rating

(1-9)*Rotation

Emerg-

ence Stand

Total Wt.

(kg)

Pod

Wt.

(kg)

Pod Wt.

(tons/A)

Cn-Cn-Cn-Bn 106 90 12.4 6.7 3.2 4.1

Cn-Bn-Cn-Bn 125 93 10.3 5.5 2.6 4.5

Bn-Bn-Bn-Bn 77 76 4.6 2.4 1.1 5.0LSD (P = 0.05) 39 16 2.3 1.3 0.6 0.6

Rotation trial with snap beansNYSAES Research Farm 2001 through 2004

*Mean rating of 40 plants dug at flowering.

Higher numbers indicate more disease pressureDr. George Abawi

Effect of incorporated cover crops on root rot severity of beans

Lower rating means better disease suppression

1 2 3 4 5 6 7 8 9

White clover ' New Zealand'

Check

Hairy vetch

White mustard 'Mantegena'

Alfalfa 'Iroquois'

Ryegrass 'Pennant'

Oats

Sudangrass

Rye grain

Wheat 'Geneva'

Crown vetch

Rapeseed

Root Rot Severity (1-9)Dr. George Abawi

0 250 500 750 1000 1250 1500 1750 2000

Hairy Vetch

Alfalfa

White clover

Rye grain

Alsike clover

Phacelia

Radish

Crown vetch

Red clover

Wheat

Oats

Buckwheat

Mustard

Ryegrass

Rapeseed

Sudex

Number of P. penetrans/g bean root

Incorporation of cover crops as green

manures against Pratylenchus penetrans

Dr. George Abawi


Manage the Host

• Resistance


• Temporally• Rotation

• Cover Cropping

Host


Disease

Plant & Microbial Diversity: Area of Active Research

General Principles

• Diversity aboveground Diversity belowground

• Diverse inputs Diverse soil community

• Diversity Robustness and Resilience• Return to proper functioning after perturbation

• Simpler communities are easier to invade & less resilient

• Diverse crops & inputs encourage beneficial organisms(cover crops, manures, green manures, composts,

vermicomposts, chitin-amended composts, etc…)

Why add different kinds of organic matter?Different types of organic matter perform different important roles

• Nutrient release (N if low C:N ratio)

• Aggregation

• Accumulation of OM in soil

• Diverse soil microbial community

• Balanced effects (over-application of same thing can be a problem)(Building Soils for Better Crops)

Beneficial Organisms and Processes Encouraged

• Antagonists of Disease

Competition for nutrients or space

Mycoparasitism

Antibiosis

Inactivation of the pathogen enzymes

Induced resistance



• PGPR• Phosphate solubilizers

• Plant hormone (mimic) producers

• ISR/SAR triggers

Biotechnol. Agron. Soc. Environ. 2011 15 (2), 327-337

http://vro.depi.vic.gov.au



• PGPR• Phosphate solubilizers

• Plant hormone (mimic) producers

• ISR/SAR triggers

• Primed nutrient cycling

• N fixers (symbiotic, associative, free-living)

• AM Fungi (with associated MHB)

Management of Soil Biota:Key Mutualisms

N Fixing Bacteria

• Transform N2 gas (unavailable) to NH3 and derivatives (plant available)

• Free-living, Associative, and Symbiotic bacteria

• Energy intensive process

Arbuscular Mycorrhizal Fungi

• Trade nutrients for sugars with plants

• Increase access to poorly available nutrients and water

• Increase disease resistance

• Contribute greatly to aggregation and OM

N Fixing Bacteria: Symbiotic

Nodulation

N Fixing Bacteria: Management

• Grow Legumes• In rotation and as cover crops• Alone or in mixtures

• Inoculate with Appropriate bacterial strains

• Check for Nodulation

• Assess Effectiveness

Cross-inoculation groups of legumes and rhizobia.

Legume group Inoculation group code Rhizobia species

Alfalfa and Sweet Clover A Rhizobium meliloti

True clovers B R. trifolii

Peas and vetch C R. leguminosarum

Soybean S Bradyrhizobium japonicum

Birdsfoot trefoil K R. loti

Crown Vetch M Rhizobium spp.

J. Grossman (on www.extension.org)

Inoculants and Effective Nodules

Importance of Soil Biota:Special Cases

N Fixing Bacteria

• Transform N2 gas (unavailable) to NH3 and derivatives (plant available)

• Free-living, Associative, and Symbiotic bacteria

• Energy intensive process


• Trade nutrients for sugars with plants

• Increase access to poorly available nutrients and water

• Increase disease resistance

• Contribute greatly to aggregation and OM

Mycorrhizae

• The normal condition for most plant roots is to be associated with symbiotic fungi – mycorrhizae are their normal joint absorptive structures

• Plant disease susceptibility is increased when this association is absent

• Conversely, disease resistance is generally increased when the plant is mycorrhizal

• Competition for infection and colonization space• Better nutrient status• Plant defenses primed – but not fighting the AMF

• AM Fungi cultivate a surrounding beneficial bacterial community

Brundrett, 1984Kinden and Brown, 1975

Arbuscules

Mycorrhizae: Function

• Mycorrhizae important for plant establishment• Particularly in mixed-species stands

• Decrease competition, increase interspecies facilitation

• Fungal diversity important for maintaining plant diversity

• Fungal growth is important for soil quality• Aggregation

• Organic Matter

• Carbon sequestration

• Harbor ‘mycorrhizosphere’ communities

• Inoculum commercially available but of extremely limited diversity

• Growing medium or in-furrow application

• Inoculation of root zone directly more useful than surface application – spores large

• Management to maintain native populations recommended

• On-farm production possible• Area of active extension work

Mycorrhizal Fungal Management


Dr. D. Douds (USDA-ARS) and Rodale Institute On-farm Arbuscular Mycorrhizal Fungal Management

Management of Key Mutualisms

AM Fungi

• Know and Grow Hosts

• Rotate

• Use Cover Crops

• Reduce Tillage

• Inoculate if Transplanting

• Don’t overload P

Rhizobia

• Inoculate Legume Seeds

• Check for (pink) nodules

• Keep pH high enough

• Keep P high enough

Wrapup / General Principles

Good environmental ConditionsConducive to plant health, not disease developmentDrainageCompactionHealthy Root Growth

Robust, Diverse Soil Biotic CommunityMainly through plant communitySome inoculation and specific

direct management possible

Target acute biological dysfunction

Best Defense is a Good Offense

management of soil biota - welcome | field crops of the soil biota •plant pathogens & disease...

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