Mark MazzolaUSDA-ARS

Tree Fruit Research LabWenatchee, Washington

Manipulation of the Soil Microbiome to Advance Orchard System Resilience

Production system:

Washington Tree Fruit

Production problem: Target-Replant Disease

‘Replant’ ‘Virgin’

Tactics to engineer the indigenous soil microbiome:

Host genetics

Soil amendments

Cover crop rhizospheremetabolites

Anaerobic Soil-Disinfestation (ASD):Brassica Seed Meal:

Manipulation of the soil microbiome:

Brassica residue amendment for disease/pest control

Evidence for a biology-based model:

Brassica seed meal (SM) induced disease suppression of multiple pathogens obtained:

• Irrespective of SM glucosinolate content (high vs. low)

• Regardless of whether a biologically active chemistry is produced

• Pathogen introduced weeks/mo after SM application fails to induce disease(suppressive soil)

Significance of chemistry vs. biological mechanisms will vary in a temporalmanner, with the target pathogen and with the seed meal type (plant origin)

Biofumigation model:

(Mazzola et al., 2002; Mazzola and Zhao, 2010; Weerakoon et al., 2012; Mazzola et al., 2015)

Glucosinolate Isothiocyanate

Sunrise orchardTreatments:

No treatment controlMustard seed meal (Brassica juncea/Sinapis alba)1,3-dichloropropene/chloropicrin fumigation (Telone C17)Planted to Gala/M9 12 May 2010

Seed meal formulation for disease control

Mazzola et al. 2015.

Gala/M9 cumulative yield (2012-13)

Seed meal formulation for disease control

Mazzola et al. 2015.

Pratylenchus penetrans

Lesion nematode root density:

plpnemweb.ucdavis.edu

Mazzola et al. 2015.

High Throughput Sequencing: Rhizosphere microbiome

Rhizosphere soil samples collected at end of second growing season at Sunrise orchard.

Similarity of rhizosphere microbiome Oct. 2011

Control Soil fumigation Seed meal

Microbial pathogens and parasites unique to seed meal treated soils

Arthrobotrys(nematode trapping)

Aporcelaimellus(omnivorous nematode)

N. Allin and G.L. Barron

J.O. Becker, J. Borneman

Dactylella oviparasitica(nematode egg parasite)

Oidiodendron(parasite of Phytophthora & Pythium)

Anaerobic Soil-Disinfestation (ASD):

Treatment protocol:

I. Incorporate a labile carbon source to stimulate microbial growth and respiration

I. Irrigate soil to field capacity

II. Tarp with virtually impermeable film

Anaerobic Soil Disinfestation (ASD): modes of action

Volatile production

Accumulation of organic acids

oxygen depletion (anaerobic environment)

Altered soil biology

Volatiles

Firmicutes

Control ASD

Influence of carbon input on ASD efficacy

Hewavitharana and Mazzola 2014

0

20

40

60

80

100

120

C Et GR SM PC RB CM

P. p

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ot

Treatment

a

a

bc bc c cb

C = ControlPC = pasteurizationEt = Ethanol GR = Orchard grassSM = Brassica juncea seed mealRB = Rice branCM = compost

Pratylenchus penetrans

plpnemweb.ucdavis.edu

47

33.2

2.2 0.8 0 00

5

10

15

20

25

30

35

40

45

50

C CM RB ET GR SM

R. s

olan

iAG

-5 ro

ot in

fect

ion

%

Carbon input

C = controlCM = compostRB = rice branET = ethanolGR = orchard grassSM = seed meal

Rhizoctonia solani

Hewavitharana and Mazzola 2014

C = ControlPC = pasteurizationEt = Ethanol GR = Orchard grassSM = Brassica juncea seed mealRB = Rice branCM = compost

Influence of carbon input on ASD efficacy

Effect of treatment on rhizosphere microbiome:

High Throughput Sequence Analysis of Microbiome:

ASD-grass

Control

ASD-compost

NMDS plot of Fungal OTU data

ASD-grass

Control

ASD-compost

NMDS plot of Bacterial OTU data

ASD-grass

Control

ASD-compost

Coprinellus curtus: controls R. solani (Nakasaki et al., 2007)Cercophora areolata: produces fungitoxic and cytotoxic compounds (Whyte et al., 1996)Gelasinospora brevispora: antifungal activity (Boonsang et al., 2014)Preussia spp.: endophyte (Mapperson et al., 2013)

Exclusive to ASD-grass

ASD may promote assembly of a disease suppressive soil microbiome

Microbiome-mediated protection against disease

ASD-Compost: Disease conduciveASD-Grass: Disease suppressive

Rhizoctonia solani

Anaerobic Soil-Disinfestation: Apple nursery replant disease field trial

RootstocksM.9 (susceptible)G.41 (‘tolerant’)G.935 (‘tolerant’)

Soil treatmentsControlASD-grassTeloneC35 fumigation

4.4003

5.2628

2.9766

FUMIGATION ASD CONTROL

Trun

k di

amet

er in

crem

ent m

m -1

Soil treatment

G41

ABA

B

4.1667

3.4173

1.9317

FUMIGATION ASD CONTROL

Trun

k di

amet

er in

crem

ent m

m-1

Soil treatment

M9

AB

C

5.77475.4423

2.696

FUMIGATION ASD CONTROL

Trun

k di

amet

er in

crem

ent m

m-1

Soil treatment

G935

A

B

A

Increase in tree caliper (diameter) over two growing seasons:

Summary:

• Active management of soil microbiome may yield more resilient cropping systems than attained in response to fumigation

• ASD and Brassicaceae SM amendment can provide fumigant levels of soil-borne disease control and yields

• Efficacy of either system relies, in part, on activity of the soil microbiome

Acknowledgements:

Shashika Hewavitharana Muditha WeerakoonLikun Wang Christian AguilarSheila Ivanov Xiaowen ZhaoDanielle Graham Michael CohenSarah Strauss Rachel LeissoAndrew Reed Parama SikdarKate Reardon Antonio Izzo

David Rudell

USDA-NIFA-SCRIUSDA-NIFA-OREIUSDA-NIFA-MBTUSDA-AFRI