Ajayasree T S seminar ppt (Microbiome engineering)


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Plant Pathology


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W elcome 1


(FAO and world bank, 2007) World s cenario of human population growth 2


Phytoremediation Disease resistance Abiotic stress tolerance Crop improvement Sustainability in agriculture 3

Microbiome engineering: current uses and future:

M icrobiome engineering: current uses and future Ajayasree. T. S. 2018-21-026 Department of Plant Pathology 4


Outline Introduction Plant and soil microbiome Steps in microbiome engineering Microbiome engineering techniques Advantages of microbiome engineering in agriculture Challenges of microbiome engineering Future thrust Summary Conclusion 5


Introduction 6 Microbiome - aggregate of all microbes and their genomes in a particular habitat ( Bulgarelli et al., 2013 )


Introduction 7 Plant microbiomes Protecting the plant from potential pathogens I mproving growth Improving health, adaptive advantages to plant Improving production (Haney et al., 2015 ) …Contd .


8 What is microbiome engineering? Balanced microbiome composition Decreased diversity Altered proportion Increased diversity Diseases/ Disorders Low fitness Slow growth Low productivity Low fertility Optimum health High fitness Fast growth High productivity High fertility Perturbation Homeostasis Dyshomeostasis (Foo et al., 2017) Microbiome engineering

Why plant microbiome engineering?:

Why plant microbiome engineering? 9 Manipulate the microbiome Optimize plant functions of interest Broad spectrum mechanisms of action Improve reliability without genetic engineering Sustainable in nature

Types of microbiome engineering:

Types of microbiome engineering 10 Plant microbiome engineering Soil microbiome engineering Human microbiome engineering Animal microbiome engineering ( Foo et al., 2017)

Plant microbiome:

Plant microbiome 11 (Haney and Ausubel , 2015) Microbial communities associated with the plant which can live, thrive, and interact with different tissues such as roots, shoots, leaves, flowers, and seeds Plant microbiome

Microbiome transfer in plants:

Microbiome transfer in plants 12 Synthetic root - associated microbiota transplant Inhibit plant diseases, resist environmental stresses, promote growth Native root - associated microbiota transplant (Foo et al., 2017)

Microbiome transfer in plants:

Microbiome transfer in plants 13 • Transfer of conducive soil microbiota • Easy to manipulate • Limited availability - functional native microbiome Native root - associated microbiota transplant (Foo et al., 2017) …Contd .

Microbiome transfer in plants:

Microbiome transfer in plants 14 …Contd . C ustomization of microbial composition Limited understanding - core microbiome Applicable to culturable microbes Synthetic root - associated microbiota transplant (Foo et al., 2017)

Soil microbiome:

Soil microbiome 15 Soil microbiome refers to microbial communities in the bulk soil beyond the rhizosphere and is mainly influenced by agricultural management practices ( Foo et al., 2017) Soil Microbiome

Overview of micro-organisms present in the rhizosphere :

Overview of micro-organisms present in the rhizosphere 16 Fungi/Oomycetes ~ 15500 genes (18 to 82 Mb) (10 5 to 10 6 per g) Archaea ~ 1300 genes (1.6 Mb) (10 7 to 10 8 per g) Protozoa ~ 14000 genes (34 Mb) (10 3 to 10 5 per g) Viruses ~ 45 genes (4 to 69 Kb) 10 7 to 10 9 per g Algae ~ 13000 genes (42 to 105 Mb) (10 3 to 10 6 per g) Nematodes ~ 18000 genes (54 to 100 Mb) (10 1 to 10 2 per g) Bacteria ~ 6500 genes (4 to 9 Mb) (10 8 to 10 9 per g) (Mendes et al . , 2013)


17 Rhizosphere microbiome the GOOD Nutrient acquisition Protection against pathogens Immune response Growth and development Tolerance to abiotic stress Physiology/ metabolism the BAD Plant diseases t he UGLY Food contamination Role of rhizosphere microbiome 17 (Mendes et al., 2013)

Engineering of soil microbiome:

Engineering of soil microbiome Implement organic farming Change land utilization Tillage Cropping systems Other agricultural practices 18 (Foo et al., 2017)

Steps in microbiome engineering:

Steps in microbiome engineering 19 Identification and culturing of potential PGPMs Deep analysis/ selection of the various components Culturing of PGPM Analysis (Woo and Pepe, 2018) *PGPM - Plant Growth Promoting Microbes

Steps in microbiome engineering:

Steps in microbiome engineering 20 Evaluate compatibility Effects in the native agroecosystem Develop formulation and distribution technology Technical support to end users ( Woo and Pepe, 2018) …Contd .

Techniques of microbiome engineering:

Techniques of microbiome engineering 21 ( Keresa et al ., 2008)

1. Host-mediated and multi-generation microbiome selection:

1. Host-mediated and multi-generation microbiome selection Cycle-dependent strategy Indirect selection-microbiomes Utilizes the host phenotype 22 ( Jochum et al., 2019)

Concept of host-mediated microbiome engineering:

Concept of host-mediated microbiome engineering 23 2) Germinate seedlings under well watered conditions 3) Expose plants to water deficiency 1) Initial microbiome inoculation 6) Repeat steps 2-4 5) Add selected rhizospheres to new sterile medium and reseed 4) Sub-select and harvest, and amalgamate the rhizospheres from the most drought resistant plants ( Jochum et al., 2019) …Contd .

Host-mediated and multi-generation microbiome selection :

Host-mediated and multi-generation microbiome selection 24 1 2 6 5 4 3 …Contd . (Mueller and Sachs, 2015)

2. Inoculation into soil and rhizosphere :

2. Inoculation into soil and rhizosphere 25 Inoculation of external strains Agrobacterium sp. 10C2 - Phaseolus vulgaris Bacillus licheniformis , Bacillus pumilus , Paenibacillus koreensis , and the genera Arthrobacter , Microbacterium , Brevibacterium ( Chihaoui et al., 2015)

3. Inoculation into seeds or seedlings :

3. Inoculation into seeds or seedlings 26 Dendrobium nobile Lindl ( Pavlova et al., 2017) Inoculation of Pseudomonas fluorescens + Klebsiella oxytoca into Dendrobium nobile Lindl seeds Growth capacity Germination Increased Adaptive capacity

Inoculation into seedlings :

Inoculation into seedlings 27 …Contd . (Rojas- Solís et al., 2018) Pseudomonas stutzeri E25 and Stenotrophomonas maltophilia CR71 into the rhizosphere of tomato seedlings Plant growth-promotion, Management of tomato gray mold Tomato seedlings

4. Tissue atomisation :

4. Tissue atomisation 28 ( Mitter et al ., 2017) Modify growth characteristics Changes endogenous microbiome of seeds - vertical inheritance Decrease in α- and γ- Proteobacteria I ncrease in β- Proteobacteria Endophytic bacterium Paraburkholderia phytofirmans PsJN into wheat and maize flowers Wheat

Tissue atomisation :

Tissue atomisation 29 …Contd . Method of tissue atomisation PsJN starts moving from embryo to germinated parts A B ( Mitter et al., 2017)

Tissue atomisation :

T issue atomisation 30 …Contd . Modified microbiome - inherited for more than one generation Plants in the second generation - not inherit the PsJN strain ( Mitter et al., 2017) Bioengineering plant microbiome without genetic manipulation

5. Direct injection into tissues or wounds:

5. Direct injection into tissues or wounds 31 ( Wicaksono et al., 2017)

Direct injection into tissues or wounds :

Direct injection into tissues or wounds 32 ( Wicaksono et al., 2017) Pseudomonas sp. R4R21AP Pseudomonas sp. T1R12P Pseudomonas sp. T1R21 Pseudomonas sp. T4MS32AP and Pseudomonas T4MS33. Endophytes Pseudomonas syringae pv . actinidiae ( Psa ) Bacterial canker of kiwifruit Leptospermum scoparium resistant to Pseudomonas syringae pv . actinidiae ( Psa ) Isolated Biocontrol agents against …Contd .

Assessment of endophytic movement:

Assessment of endophytic movement 33 …Contd . Foliar sprays - inoculate endophytic bacteria ( Wicaksono et al., 2017)

Inhibition mechanism :

Inhibition mechanism 34 ( Wicaksono et al., 2017) …Contd . Pseudomonas sp. T1R12P Pseudomonas sp. T1R21 Dual culture assay

Inference of study:

Inference of study 35 Inhibition of Pseudomonas syringae pv . actinidiae biovar 3 of kiwi plants R educed pathogen population Disease management by single application …Contd . ( Wicaksono et al., 2017)


36 Microbiomes Plants 3. Phytoremediation Plant growth enhancement Role of Signaling (Tian et al., 2020) 5. Salinity stress tolerance Advantages of microbiome engineering in agriculture Drought stress tolerance Disease stress tolerance


37 1. Drought stress tolerance


38 SI. No. Microbes Crop Mechanisms References I Bacterial - phytohormone modulators 1. Rhizobium leguminosarum LR-30, Mesorhizobium ciceri CR-30 and CR-39 & Rhizobium phaseoli MR-2 Wheat IAA improved growth, biomass Hussain et al., 2014 II Bacterial - ACC deaminase ( ACCd ) producers 2. Burkholderia phytofirmans , Enterobacter sp . Maize Increases chlorophyll content Naveed et al., 2014 III Bacterial - exopolysaccharide producers 3. Pseudomonas putida, Rhizobium sp. Sunflower EPS Alami et al., 2000 Mechanisms of drought tolerance

Drought tolerance by microbiome engineering:

Drought tolerance by microbiome engineering 39 ( Jochum et al., 2019)

Effect of HMME on drought tolerance :

Effect of HMME on drought tolerance 40 …Contd . *HMME: Host-Mediated M icrobiome E ngineering ( Jochum et al., 2019)

Effect of HMME on wheat seedlings under drought stress:

Effect of HMME on wheat seedlings under drought stress 41 ( Jochum et al ., 2019) …Contd . Sterile rhizosphere soil Non-sterile rhizosphere soil

Inference of study:

Inference of study 42 A lter rhizosphere microbiome Drought stress symptoms onset delayed - 10 th to 15 th day Plant biomass, root dry weight, root length Soil aggregation, water holding capacity Less per cent water loss Reduction in alphaproteobacteria Increase of betaproteobacteria …Contd . ( Jochum et al., 2019)


SI. No. Plant Microbiome Stress Effects References 1. Arabidopsis thaliana Xanthomonas sp. WCS2014-23 , Stenotrophomonas sp. WCS2014-113, Microbacterium sp. WCS2014-259 Hyaloperonospora arabidopsidis Less fungal spores, higher plant fresh weight Berendsen et al., 2018 2. Potato Pseudomonas spp. R32, R47, R76, R84, S04, S19, S34, S35, S49 Phytophthora infestans Reduced fungal sporangiophore development Vrieze et al., 2018 3. Tomato Pseudomonas spp. CHA0, PF5, Q2-87, Q8R1-96, 1M1-96, MVP1-4, F113, Phl1C2 Ralstonia solanacearum Reduced disease severity, pathogen abundance Hu et al., 2016 43 2. Disease stress tolerance

3. Phytoremediation:

3. Phytoremediation 44 Betula celtiberica 54 culturable rhizobacteria and 41 root endophytes Metal plant accumulation Phytoremediation Birch tree ( Betula celtiberica ) (Mesa et al., 2017) Against arsenic toxicity

Mechanisms of phytoremediation:

Mechanisms of phytoremediation 45 plant growth by bacterial metabolites Plant growth by bacterial metabolites - IAA Metal chelation by siderophores Organic acid production Phosphate solubilisation ACCD activity (Mesa et al., 2017 ) …Contd . Neorhizobium sp. Rhizobium sp. Variovorax sp. Phyllobacterium sp. Rhodococcus sp. Aminobacter sp. Ensifer adhaerens

4. Plant growth enhancement:

4 . Plant growth enhancement 46 (Kong et al., 2018) High quality crops High -throughput sequencing Root associated microbiome KOMODO: predict microbial culture media Core microbial taxa and hubs Network analysis Biofertilizer Microbial consortium PGP activities Microbial synergism Dyanamic changes Artificial construction of synthetic microbial consortia Ecological evaluation Efficacy assessment

5. Salinity stress tolerance:

5. Salinity stress tolerance 47 Saline soil - EC ˃ 4 dS m -1 Deteriorated growth N itrogen content P hotosynthetic capacity M etabolic processes Maize ( Upadhyay et al ., 2011)

Microbiome against salinity…:

Microbiome against salinity… 48 SI. No. Microbiome Crops References 1. Serratia sp.+ Rhizobium sp. Lettuce Han and Lee, 2005 2. Rhizobium tropici (CIAT899) or R. etli (ISP42) + Ensifer fredii SMH12, HH103 + Chryseobacterium balustinum Aur9 Common bean, Soybean Estevezi et al., 2009 3. Pseudomonas sp. + Rhizobium sp. Maize Bano and Fatima, 2009 4. Bacillus sp. + Burkholderia sp. + Enterobacter sp. + Microbacterium sp. + Paenibacillus sp. Wheat Upadhyay et al., 2012 5. Brachybacterium saurashtrense (JG-06) + Brevibacterium casei (JG-08) + Haererohalobacter (JG-11) Ground nut Shukla et al., 2012 …Contd .

6. Role of signaling molecules:

6 . Role of signaling molecules 49 Administration of root exudates e.g . salicylic acid Resist environmental stresses, promote growth Promote - balanced microbiome Limited availability - signaling molecules (Foo et al., 2017)


50 Environmental factors Plant phenotype Plant genotype, Plant age Factors influencing plant microbiome engineering ( Compant et al., 2019) Agricultural management Soil characteristics Abundance, diversity, functionality, and colonization of microorganism in above- and below- ground plant parts

Challenges of microbiome engineering:

Challenges of microbiome engineering Effect of abiotic or environmental factors Deeper understanding of the microbial community structure over time Limited ability to harness and manipulate the microbiome in agriculture N ature and mechanisms of microbiota-plant relationship Bridging the lab-field gap 51


Summary 52 Microbiome engineering enhances sustainability in agriculture Steps in microbiome engineering Various techniques for microbiome engineering Advantages of microbiome engineering Factors influencing microbiome engineering Challenges of microbiome engineering

Future thrusts:

Future thrusts Microbiome manipulation by plant Identification of stable, stress tolerant microbiomes Develop more microbial consortia 53


Conclusion 54 “ I play with microbes. There are of course, many rules to this play… but when you have acquired knowledge and experience it is very pleasant to break the rules and to be able to find something nobody has thought of ˮ Alexander Fleming

Thank you:

Thank you 55

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