Temporal Changes in Soil Microbiome in Response to Soil ...€¦ · Soil Microbial Communities and...
Transcript of Temporal Changes in Soil Microbiome in Response to Soil ...€¦ · Soil Microbial Communities and...
Temporal Changes in Soil Microbiome in Response to Soil TreatmentsShashika S. Hewavitharana PhD
Assistant Professor
Horticulture and Crop Science Department
Cal Poly State University San Luis Obispo
Gulya et al. 2006
https://ucanr.edu/
Microbiome is ubiquitous
bacteria of the human gut microbiome
Credit: Wyss Institute at Harvard University
community of bacteria from human nose
Credit: Steve Gschmeissner/SPL
Temporal Changes in Skin Microbiome
Oh et al., 2016, Cell 165, 854–866
Soil Microbial Communities and Molecular Interactions
Jansson and Hofmockel, 2018Current Opinion in Microbiology 2018, 43,162–168
• Supporting interdisciplinary research to answer fundamental questions about microbiomes in diverse ecosystems.• Developing platform technologies that will generate insights and
help share knowledge of microbiomes in diverse ecosystems and enhance access to microbiome data.• Expanding the microbiome workforce through citizen science and
educational opportunities.
Source: https://obamawhitehouse.archives.gov/
Appl
es • ~68% national production in WA (NASS, 2019)
• ~90% of national organic crop in WA (NASS, 2016)
• Value ~$ 2.2 billion
Stra
wbe
rrie
s • ~90% of the national production in CA (NASS, 2019)
• ~98% of the crop value of organic strawberry in CA (NASS, 2016)
• Value $2.9 billion
Extent of the Industries
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Apple replant disease
• Caused by a pathogen complex– Rhizoctonia solani AG-5, AG-6– Cylindrocarpon spp.– Pythium spp.– Phytophthora cactorum– Pratylenchus penetrans
http://www.ces.ncsu.edu
Disease symptoms
Manson, WAMoxee, WA
Courtesy Mark Mazzola
Soil-borne Pathogens of Strawberrya. Fusarium wilt - Fusarium oxysporum f. sp. fragariae
b. Macrophomina crown rot - Macrophomina phaseolina
c. Verticillium wilt - Verticillium dahliae
d. Phytophthora crown rot - Phytophthora spp.
a http://ucanr.edu b http://ucanr.edu c http://www.omafra.gov.on.ca https://pnwhandbooks.orgd
Need of alternatives for disease management
• Emergence of new soilborne diseases• Restrictions on soil fumigation• Demand for long-term disease control • Increasing extent of organic industry
Anaerobic Soil Disinfestation (ASD)
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Anaerobic Soil Disinfestation (ASD)
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Grass application Amending into soil Irrigation
Tarping Tarp Removal
C source Rate /acre Irrigation Cost ($) acre -1
Rice bran (RB) 2 t Field capacity 240
Brassica juncea seed meal (SM)
2 t Field capacity 3200
Grass clippings (GR)(Dactylis glomerata L.)
9 t Field capacity Mowing + spread
Composted steer manure (CM)
4.5 t Field capacity 153
Ethanol (ET) 80 gal ½ Field capacity 900
ASD Carbon SourcesTreatments after one
week incubation
Soil amendment rates 13
Fungal growth after ASDin treated orchard soil
Ethanol Control Pasteurized Grass clippings
Composted Steer manure
Rice bran
Brassica juncea seed
meal
Resident soil microbiome changes
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0
0.5
1
1.5
2
C ET GR SM RB CM
Seed
ling
wei
ght/
g
C treatment
b b
aa
b b
R. solani AG-5
Fung
al C
omm
unity
Bact
eria
l Com
mun
ity
C source
Rice bran (RB)
Brassica junceaseed meal (SM)
Grass clippings (GR)
Composted steer manure (CM)
Ethanol (ET)
Hewavitharana and Mazzola, 2016
Experimental Set-up
(Swenson et al. 2015)
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Day
0
Day
1
Day
2
Day
3
Day
7
Day
11
Day
15
Control
ASD Soil DNA
Illumina® sequencing
Polar and non-polar metabolite analysis
Volatile analysis
Swenson et al. 2015
5,634 OTUs
689 metabolitesHewavitharana et al. 2019
Changes in O2 and CO2 levels in the Headspace
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0
5
10
15
20
25
30
35
0 50 100 150 200 250 300 350 400
Rela
tive
head
spac
e co
ncen
trat
ion
(%)
Hours after set-up
O2 ASD O2 Control CO2 ASD CO2 Control
Day1
5----
-<---
Day0
Day0---------->--------Day15
Day1
5----
--<---
-----D
ay0
Day0--------->---------Day15ASD
ASD
Cont
rol
Control
Bacteria
Similar
Dissimilar
Fungi
Day1
5----
--<---
-----D
ay0
Day1
5----
-<---
Day0
Cont
rol
ASD
Changes in Soil Microbiome
18Similar
Dissimilar
Changes in Relative Abundance of Bacterial Divisions
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0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
ASD.
Day0
.Rep
1.
ASD.
Day0
.Rep
2.
ASD.
Day0
.Rep
3.
ASD.
Day0
.Rep
4.
ASD.
Day0
1.Re
p1.
ASD.
Day0
1.Re
p2.
ASD.
Day0
1.Re
p3.
ASD.
Day0
1.Re
p4.
ASD.
Day0
2.Re
p1.
ASD.
Day0
2.Re
p2.
ASD.
Day0
2.Re
p3.
ASD.
Day0
2.Re
p4.
ASD.
Day0
3.Re
p1.
ASD.
Day0
3.Re
p2.
ASD.
Day0
3.Re
p3.
ASD.
Day0
3.Re
p4.
ASD.
Day0
7.Re
p1.
ASD.
Day0
7.Re
p2.
ASD.
Day0
7.Re
p3.
ASD.
Day0
7.Re
p4.
ASD.
Day1
1.Re
p1.
ASD.
Day1
1.Re
p2.
ASD.
Day1
1.Re
p3.
ASD.
Day1
1.Re
p4.
ASD.
Day1
5.Re
p1.
ASD.
Day1
5.Re
p2.
ASD.
Day1
5.Re
p3.
ASD.
Day1
5.Re
p4.
Perc
enta
ge o
f lib
rary
Incubation duration
VerrucomicrobiaThermotogaeThermodesulfobacteriaTenericutesSynergistetesSpirochaetesProteobacteriaPlanctomycetesNitrospiraeNitrospinaeIgnavibacteriaeGemmatimonadetesFusobacteriaFirmicutesFibrobacteresElusimicrobiaDeinococcus_thermusDeferribacteresCyanobacteriaChloroflexiChlorobiChlamydiaeCandidatus saccharibacteriaBacteroidetesArmatimonadetesAquificaeActinobacteriaAcidobacteria
Changes in Relative Abundance of Fungal Divisions
20
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
ASD.
Day0
.Rep
1
ASD.
Day0
.Rep
2
ASD.
Day0
.Rep
3
ASD.
Day0
.Rep
4
ASD.
Day0
1.Re
p1
ASD.
Day0
1.Re
p2
ASD.
Day0
1.Re
p3
ASD.
Day0
1.Re
p4
ASD.
Day0
2.Re
p1
ASD.
Day0
2.Re
p2
ASD.
Day0
2.Re
p3
ASD.
Day0
2.Re
p4
ASD.
Day0
3.Re
p1
ASD.
Day0
3.Re
p2
ASD.
Day0
3.Re
p3
ASD.
Day0
3.Re
p4
ASD.
Day0
7.Re
p1
ASD.
Day0
7.Re
p2
ASD.
Day0
7.Re
p3
ASD.
Day0
7.Re
p4
ASD.
Day1
1.Re
p1
ASD.
Day1
1.Re
p2
ASD.
Day1
1.Re
p3
ASD.
Day1
1.Re
p4
ASD.
Day1
5.Re
p1
ASD.
Day1
5.Re
p2
ASD.
Day1
5.Re
p3
ASD.
Day1
5.Re
p4
Perc
enta
ge o
f lib
rary
Incubation duration
ZygomycotaNeocallimastigomycotaMonoblepharidomycotaGlomeromycotaEntomophthoromycotaCryptomycotaChytridiomycotaBasidiomycotaAscomycota
Changes in Relative Abundance of Classes of Division Ascomycota
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0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
ASD.
Day0
.Rep
1
ASD.
Day0
.Rep
2
ASD.
Day0
.Rep
3
ASD.
Day0
.Rep
4
ASD.
Day0
1.Re
p1
ASD.
Day0
1.Re
p2
ASD.
Day0
1.Re
p3
ASD.
Day0
1.Re
p4
ASD.
Day0
2.Re
p1
ASD.
Day0
2.Re
p2
ASD.
Day0
2.Re
p3
ASD.
Day0
2.Re
p4
ASD.
Day0
3.Re
p1
ASD.
Day0
3.Re
p2
ASD.
Day0
3.Re
p3
ASD.
Day0
3.Re
p4
ASD.
Day0
7.Re
p1
ASD.
Day0
7.Re
p2
ASD.
Day0
7.Re
p3
ASD.
Day0
7.Re
p4
ASD.
Day1
1.Re
p1
ASD.
Day1
1.Re
p2
ASD.
Day1
1.Re
p3
ASD.
Day1
1.Re
p4
ASD.
Day1
5.Re
p1
ASD.
Day1
5.Re
p2
ASD.
Day1
5.Re
p3
ASD.
Day1
5.Re
p4
Perc
enta
ge o
f lib
rary
Incubation duration
xylonomycetes
sordariomycetes
schizosaccharomycetes
saccharomycetes
pezizomycotina
pezizomycetes
orbiliomycetes
leotiomycetes
lecanoromycetes
eurotiomycetes
dothideomycetes
ascomycota
arthoniomycetes
archaeorhizomycetes
Temporal Changes in Soil Microbiome and Metabolome in Response to ASD
Microbiome shifts Metabolome shifts
Bacterial Community Fungal Community
Hewavitharana et al. 2019
Co-abundance Correlation Microbial Network-ASD treatment
Hewavitharana et al. 2019
Co-abundance Correlation Metabolite Network-ASD treatment
Hewavitharana et al. 2019
Volatile acids, aldehydes, alcohols, and hydrocarbons produced during simulated anaerobic
soil disinfestation (ASD)
Hewavitharana et al. 2019
Key Functional Attributes of ASD
Hewavitharana et al. 2019
Host challenged by the pathogen complex of replant disease
Enhanced host growth and long-term disease suppression by managing rhizosphere microbiome and metabolome
Anaerobic soil disinfestation
Induced proliferation of beneficial microorganis
ms
Anaerobiosis Competition
Toxic volatiles and
metabolites
How does ASD Work?
Mazzola and Hewavitharana, 2019
Temporal Changes in Soil Microbiome in Response to Soil Fumigation in Strawberry
Production Systems
Objectives:
• Study temporal changes in microbiome� Post-treatment� At planting� One month after planting� At peak fruit production� End of the season
• Identify biomarker organisms that could be targeted for enrichment
https://ucanr.edu/
Post-treatment Soil SamplingFumigant/Treatment Active IngredientsAlly 33 Allyl Isothiocyanate (64%), Chloropicrin (31%)Dominus Allyl Isothiocyanate (96%)K-Pam HL Potassium N-Methyldithiocarbamate (54%)Tri-Clor Chloropicrin (99%)No-treatment Control NA
Transplanting in July 2019
Effect of Soil Treatments on V. dahliae Soil Population
0
1
2
3
4
5
6
7
8
9
Vert
icill
ium
dah
liae
CFU
g-1
soil
Soil treatment*time point
0.00
0.50
1.00
1.50
2.00
2.50
3.00
3.50
4.00
Vert
icill
ium
dah
liae
CFU
g-1
soil
Soil treatment*(Time point 1-Time point 2)
Effect of Soil Treatments on Plant Mortality
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
Ally Dominus KPAM Triclor Control
Perc
ent p
lant
mor
talit
y
Soil treatment
11/7/2019
11/23/2019
12/12/2019
1/5/2019
Marketable Yield Differences among Treatments
0.000
0.005
0.010
0.015
0.020
0.025
Ally33 Dominus K-PAM Tri-Clor Control
Yiel
d pl
ant-1
kg-1
Soil treatment
30-Oct
15-Nov
Concluding Remarks
• Biology mediated soilborne disease management is complex• Efficacy of ASD is dependent on various factors that need to be
tailored based on the pathosystem• ASD mediated disease suppression is connected to interaction
between soil microbiome and metabolome• Potential for identifying beneficial microorganisms after soil
fumigation that can be enriched with additional practices
• Dr. Mark Mazzola, Dr. David Rudell, Dr. Jim Mattheis, Dr. Loren Honaas, Dr. Rachel Leisso- USDA-ARS Wenatchee• Dr. Gerald Holmes, Dr. S. Mansouripour, Kyle Blauer, Drew Summerfield,
Farm crew- Cal Poly Strawberry Center• Cal Poly Students: Olivia Mann, Maria Debaros, Abby Maxwell, Maria
Sanchez, Angela Cruz, Lauren Tallichet• Funding agencies and industry partners:
Acknowledgement
Thank you
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