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Factors Shaping the Root-Associated Microbiome of Populus species. Christopher W. Schadt Oak Ridge National Laboratory & University of Tennessee - Knoxville. Plant-Microbe Interfaces. Aim 1: Define. Aim 2: Dissect. fungi. plants. bacteria. Natural Systems. Components. - PowerPoint PPT Presentation
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Factors Shaping the Root-Associated Microbiome of Populus species
Christopher W. SchadtOak Ridge National Laboratory &University of Tennessee - Knoxville
Natural Systems Components
Aim 1: Define Aim 2: Dissect
plantsfungi
bacteria
Interactions & Signaling
Plant-Microbe Interfaces
Caney Fork River, TN
Yadkin River, NC
PMI Plant-Microbe Interactions: Genotype & Environment Interactions in Structuring the Populus Microbiome
Populus deltoides (2009-2011 Campaigns)
Populus trichocarpa (2012 & Beyond)
Studies focused on broad associations of microbiome patterns within natural riparian populations in the Southeast.
Studies of common-garden GWAS populations that will allow examination of detailed genome-level associations between host & microbiome
Gottel, NR, et al. (2011). Populus deltoides roots harbor distinct microbial communities within the endosphere and rhizosphere across contrasting soil types. Appl. Environ. Microbiol. 77, 5934-5944.
Objective:
Assess the composition and variability within and between, endosphere and rhizosphere communities
Campaign 1: Caney Fork Study of Upland and Bottomland Root Endophyte and Rhizosphere
Communities
N. Gottel H. Castro
Endosphere and rhizosphere communities are distinct regardless of origin from upland or
bottomland sites
Fungi
PCA analysis shows distinct endophyte and rhizosphere communities regardless of upland or bottomland origin
BacteriaEndo|Rhizo
FungiEndo|Rhizo
Hierarchical clustering of OTUs also shows most appear specialized to either the rhizosphere or endosphere niche, and are rarely in abundance in both
Caney Fork River, TN
Yadkin River, NC
Campaign 2: A P. deltoides regional studyObjectives• Verify the separation
between the endosphere and rhizosphere microbial niches
• Examination of seasonal effects on microbiome structure
• Test the effects of soil and host characteristics across a broad range of natural conditions
M. Shakya W. Muchero H. Castro
P. deltoides genotypes and soils from TN and NC are diverse, but covary by region• Soils exhibit a wide range of variation. pH, organic matter, nitrogen,
and soil texture vary widely across the sites• SSR genotyping of trees shows a variation in population structure with
division between samples originating from different regionsSoil texture across sites Plant genotypes across sites
NMDS analyses of Caney Fork and Yadkin datasets show partitioning by sample type and region• Rhizosphere/
Endosphere divide is confirmed
• Variability between endophyte samples is extreme (but diversity low)
• Structure according to regional origin and season is also significant
• Variance partitioning between a suite of host and environmental factors explains only 33% to 56% of community-wide microbiome variation
• Within Phyla & and dominant OTUs more significant trends are observed
Disentangling the drivers of community patterns remain an elusive task
Fungi Bacteria
Common garden / GWAS populations of Populus trichocarpa in the Pacific Northwest• 1100 variants of P.
trichocarpa collected across it’s latitudinal range replicated in four common gardens in BC, OR and CA
• >900 of these have been resequenced to at least 12X depth by JGI.
G. TuskanW. Muchero
2012 CSP project examining associations of host characteristics and the root microbiome • Pathogen Susceptibility
(Meampsora infection rates)• Copy number variation
(Lectin Receptor Kinase)
• Plant Growth (Biomass)
• Secondary Chemistry (Lignin S:G)
Larger scale of analyses facilitated by new JGI collaboration via 2012 CSP program• Combination of large scale rRNA community profiling multiplexed on
MiSeq Illumina system (all samples, all traits)- 8 genotypes selected at extremes for 4 traits (32 genotypes)- 32 genotypes w/ 3 replicates in 2 locations (192 trees)- Endophyte, rhizospshere & bulk soil samples (576 samples)- Bacterial, fungal & archaeal community (1728 rRNA profiles)
• In depth metagenomic profiles using 32 lanes of HiSeq Illumina profiling (select sample/trait)
a-Proteobacteria
b-Proteobacteria
BacilliBacteroidetes
• Isolated 2800+ bacteria & 900+ fungi
• 43 bacterial isolates have been sequenced from P. deltoides with a concentration on Pseudomonas
• 6 fungal isolates underway through various JGI programs
g-Proteobacteria
Conserved among our iso-lates and ref-erence organ-
isms, 1535, 52%Conserved in
our isolate organisms, 969, 33%
Found in some of our isolates only, 426, 15%
2930 predicted KEGG orthologous groups in 21 Pseudomonas isolates and 4 reference spp.
D. Pelletier S. Brown
What is the genomic and functional diversity within Populus isolates?
S. Utturkar
R. Vilgalys G. Bonito T. Karpinets
Pseudomonas spp. show high functional diversity
TREE ECO-UNIT STRAIN Anti QS Sid Prot Phos IAA(ug/ml) NO3 MHBB1B endophyte Pseudomonas GM17 2 high + + - 0.2 + neg
B1B endophyte Pseudomonas GM21 neg neg + - - 2.4 - o
B4A rhizosphere Pseudomonas GM49 1 neg + - - 0.1 - o
B4A rhizosphere Pseudomonas GM48 1 neg + + - 0.1 - +B2B endophyte Pseudomonas GM33 1 neg + - + 1.0 - +
U2A rhizosphere Pseudomonas GM74 1 neg + - - 1.0 - o
B4B endophyte Pseudomonas GM55 neg neg + - + 1.5 - o
B3B endophyte Pseudomonas GM41 1 neg + + + 1.5 + +
B1B endophyte Pseudomonas GM18 1 low + + + 0.6 - +
B4B endophyte Pseudomonas GM50 2 low + + + 1.0 - o
U3B endophyte Pseudomonas GM102 1 neg - + 0.9 - o
U2B endophyte Pseudomonas GM79 2 neg + + - 2.2 + +
B2B endophyte Pseudomonas GM30 3 med + ++ - 0.9 - o
B4B endophyte Pseudomonas GM24 4 neg + ++ - 1.5 - negB1B endophyte Pseudomonas GM16 3 neg + ++ + 1.4 - neg
B2A rhizosphere Pseudomonas GM25 1 neg + + + 0.8 - o
soil Pseudomonas fluorescens PfO1 ND ND ND ND ND ND ND ND
U2B endophyte Pseudomonas GM80 1 neg + ++ - 0.9 - o
B4B endophyte Pseudomonas GM60 neg neg + + - 0.9 + o
U1B endophyte Pseudomonas GM67 1 neg + - - 1.0 + o
U2B endophyte Pseudomonas GM78 1 neg + - + 1.3 - o Cotton root Pseudomonas fluorescens Pf5 2 ND + + + 0.1 neg
U3A rhizosphere Pseudomonas GM84 1 neg + - + 1.7 - o
endophyte Pseudomonas putida W619 ND ND ND ND ND ND ND ND pathogen Pseudomonas syringae DC3000 ND ND ND ND ND ND ND ND
ORNL
Often same types of endophytic isolates seen across Populus (ORNL) and Arabidopsis
(Dangle)
UNC
Sur Paredes
AcknowledgementsSchadt Lab at ORNLMigun ShakyaMike RobesonZamin YangNeil GottelHector CastroMarilyn Kerley
ORNL CollaboratorsJerry TuskanMitch DoktyczDale PelletierMircea PodarJessy L. LabbéWellington MucheroTatiana KarpinetsSteven BrownSagar Utturkar
JGISusannah TringeStephanie MalfattiTijana Glavina del Rio
Duke UniversityRytas VillgalysGregory BonitoKhalid HameedJay KrishnanMichael GajdeczkaAndrii Grygansky
INRAFrancis Martin