Arcand, M.

Bell, J.

Dowhy, T.

Helgason, B.

Lamb, E.

Mamet, S.

Morales, Z.

Shirtliffe, S.

Siciliano, S.

Taye, Z.M.

Vail, S.

Williams-Johnson, S.

English

University of Saskatchewan Research Archive

beneficial plant-microbial interactions in agroecosystems: deciphering the rhizosphere microbial community in two field grown cropsZelalem Mengiste TayePhD Student2018 Soils and Crops Conference March 6, 2018Co-AuthorsDr. Eric LambDr. Bobbi HelgasonDr. Sally VailDr. Steven SicilianoDr. Melissa ArcandDr. Steve ShirtliffeAlix SchebelSummer lab and field crews Many othersDr. Steven MametTanner DowhyJenifer BellShanay Williams-JohnsonZayda MoralesAcknowledgmentCanola Lines Show Variation in Selecting their Rhizosphere Bacterial Members2018 Soils and Crops Conference March 6, 2018IntroductionPlant Microbiome▪ Rhizosphere▪ Alter soil microbes▪ Source of geneticvariabilityMurial and Alka, 2016Objectives▪ Characterize the core microbiome of Brassica napus(Canola).▪ Identify bacterial taxa (SNVs) that are differentiallyabundant among Canola lines.Methods▪ DNA sequencing ▪ Samples ▪ Extraction▪ “Universal primers” ▪ Amplify 16S rRNA▪ Gene ▪ NG Sequencing▪ Match to a databaseHow are microbes studied?MethodsProcessing raw sequence readsSequence (SNV) and Taxonomy tableTrimommatic (Bolger et al., 2014)Cutadapt (Marcel, 2011)DADA2 (Callahan et al., 2016)http://2016.igem.org/Team:Dalhousie_Halifax_NS/DescriptionMethodsExperimental Design• Experimental site : Llewelyn Famrn nearSaskatoon, SK• Oilseed … wheat … barely … and fallow• Sixteen canola (Brassica napus) lines• Design: RCBD with three blocks + three reps• Sampling: weekly for ten weeksMethodsStatistical Analysis▪ Core Microbiome:▪ Phyloseq R package (McMurdie and Holmes, 2013)▪ Microbiome R package (Leo et al., 2017)▪ Detection threshold of 0.1 and prevalence 50 to 95 %▪ Differential abundance▪ DESEQ2: phyloseq extention (Love, Huber, and Anders 2014)▪ Generalized linear model with negative binomial distribution▪ False discovery rate of 1% (alpha value of 0.01)▪ P value :Benjamini-Hochberg (BH) adjustment (Benjamini and Hochberg1995)ResultsMajor Bacterial Taxa in Canola Rhizosphere▪ 49526 taxa in 6 taxonomic ranks39 DAPFlowering start60 DAPFlowering endResultsMajor Bacterial Taxa in Canola Rhizosphere▪ 49526 taxa in 6 taxonomic ranksResultsMajor Bacterial Taxa in Canola Rhizosphere by Canola LineResultsCore Microbiome of CanolaPrevalence 50 60 65 75 80 85 90 95# Core taxa 39 23 16 8 5 4 2 1• Of observed 49526 tax• At 90%:• Pseudarthrobacter (Actinobacteria)• Bradyrhizobium (Proteobacteria)ResultsCore Microbiome of Canola (75%)Phylum GenusProteobacteria StenotrophomonasProteobacteria BradyrhizobiumProteobacteria SkermanellaProteobacteria SkermanellaActinobacteria PseudarthrobacterActinobacteria ArthrobacterActinobacteria unclassifiedAcidobacteria unclassifiedResultsCore Microbiome of CanolaCore MicrobiomeCo-occurrence PatternMicrobial hubResultDifferential Abundant Bacterial Taxa▪ Number of differentially abundant taxa in fifteenCanola lines compared with the reference line▪ False discovery rate of 1% (Adj. p value < 0.01)L2 L3 L4 L5 L6 L7 L8 L9 L10 L11 L12 L13 L14 L15 L16L1 273 476 193 375 223 214 274 239 220 274 226 230 244 279 204ResultDifferential Abundant Bacterial Taxa▪ Significantly differential abundant bacterial taxa in Line 2 at a falsediscovery rate of 1 %Up: 156Down: 117ResultDifferential Abundant Bacterial Taxa▪ Significantly differential abundant bacterial taxa in Line 2 at a false discovery rate of 1 %Up: 156Down: 117PedobacterPGPStenotrophomonasantifungal activityAetherobacterAlleviating salt stressRhodoplanesActiveDighten et al., 2014; Berg et al. 1996 ; Fan et al. 2016 ; Gkarmiri et al 2017Take Home Message▪ Rhizosphere Microbiome can be potentialsource of genetic variability need forbreeding the next generation Canolaverities.THANK YOUQuestions?

Beneficial plant-microbial interactions in agroecosystems: deciphering the rhizosphere microbial community in two field grown crops

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Beneficial plant-microbial interactions in agroecosystems: deciphering the rhizosphere microbial community in two field grown crops

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