24/4 - microbe interaktions Flashcards
Why study plant beneficial microbes?
Support food security and food safety!
Yield loss of crops due to; abiotic and biotic stress,
nutritional deficiency,….
Supportive agrochemicals often synthetic…
Toxic products in attacked plants (plant or pest origin).
Organic (”durable”) production need novel tools.
By understanding how plants can interact with beneficial
microbes more sustainable crop plant production could be achieved and contribute to circular bioeconomy
Naturally occurring microbes in soil - vilka finns
Bacteria, archaea, protozoa, yeasts, filamentous fungi
hur spelar jorden in när det kommer till microbial profiles
Different soils different microbial profiles
hur mycket bakterier finns i jorden
1 gram of soil contain >109 bacteria of >107 taxa.
hur utvecklas det till en microbe interaktions
Parasitism – commensalism - mutualism.
Beneficial microbes has co-evolved with (specific) plant hosts.
Microbiota - microbiome
Microbiota: taxonomic description of a community
Microbiome: funktional description of a community - can använda fysiolocal tools men idag använd mest dna sequensing
Dessa används ofta som samma sak men det är inte sant
Ecosystem service - vad?
promote growth & stress tolerance of plants
Hur kan microberna i en växt variera
Beror på var på växten de finns
What is the nature of the natural plant microbiome?
Arabidosis root/leaf microbiome - relative abundance of bacterial phyla!
How to characterize soil microbiomes?
- Cultivation in vitro – total – specific media
- Metagenomics
- Targeted sequencing
- Fingerprinting
How to characterize soil microbiomes?
- Cultivation in vitro – total – specific media
- Metagenomics
- Targeted sequencing
- Fingerprinting
Biofertilizer def
A substance that contains live microorganisms
which, when applied on the seed, plant surface
or soil, colonizes the rhizosphere and promote
plant growth through increased supply of primary
nutrients for the host plant
Phytostimulator def
Microorganism, with the ability to produce
phytohormones such as indole acetic acid,
gibberellic acid, cytokinins and ethylene
Biopesticide (Biocontrol agent) def
Microorganisms that promote plant growth
by controlling phytopathogenic agents
Biostimulant
US Farm Bill 180417 USDA “a substance or micro-organism that
when applied to seeds, plants, or the rhizosphere, stimulates natur
processes to enhance or benefit nutrient uptake, nutrient efficiency,
tolerance to abiotic stress, or crop quality and yield.
Most studied PGPR/PGPF/biocontrol agents (BCA) are strains of e.g
Trichoderma, Pseudomonas, Bacillus
Vad är bra med PGPR
PGPR increase plant vigour that improve stress management.
PGPR can also act as Biocontrol agents (BCA) to improve pest resistance
through priming of Induced Systemic Resistance (ISR).
PGPR may also improve abiotic stress tolerance by priming of Induced
Systemic Tolerance (IST).
Vad är bra med PGPR
PGPR increase plant vigour that improve stress management.
PGPR can also act as Biocontrol agents (BCA) to improve pest resistance
through priming of Induced Systemic Resistance (ISR).
PGPR may also improve abiotic stress tolerance by priming of Induced
Systemic Tolerance (IST).
Priming of plant defense to abiotic and biotic stress
Certain chemicals or microbes can prime plant defense.
Sensitization – more rapid and stronger defense upon challenge.
Primed defense is activated only after stress challenge.
Priming agents have low fitness costs in the absence of stress.
For PGPR effect - colonisation/biofilm formation on roots is important.
ISR/IST protection seems long lasting.
Transgenerational?
Why not maximal growth and defense for plants?
är en våg mellan defence och growth/reproduction
- var energin ska få
Complex
hormonal
interplay
PRRs
pattern recognition receptors) located on the cell surface are specific to
different compound classes
PRR binding initiate-elicit plant defense.
Pathogens cause PTI, ETS, ETI.
Conserved microbial elicitors called pathogen-associated molecular patterns (PAMPs) are
recognized by pattern recognition receptors (PRRs). Perception may involve recognition by
intracellular receptors of pathogen virulence molecules called effectors, which causes effectortriggered
immunity (ETI) or effector triggered susceptibility (ETS). Co-evolutionary dynamics
between plants and pathogens differ. PTI and ETI give similar responses.
MAMP
beneficial microbes
How do beneficial microbes (MAMP) become accepted by a plant?
Roots & exudates determine
interactions with other plants
& soil microbiota.
Plant root colonization – critical step to enable successful priming
Plant root colonization by bacteria often followed by biofilm formation
Biofilm produktion
The underground environment is complex and competetive. Good rhizosphere competence is needed for PGPR/BCA. The biofilm embed the bacteria on the rhizoplane and avoid exposure to other microbes. The role of root border cells produced by plants are unclear in this process. Root border cells are suggested to be used to trap certain pathogens by exudation of DNA and other compounds.
Biological control of pathogens depend on different factors
effecter
Direct effect antagonism hyperparasitism/predation antibiosis lytic enzymes interference (signalling,...)
Indirect effect
competition
host plant growth promotion
improved host resistance
ISR
Induced Systemic Resistance
Priming of plant defense (Induced Systemic Resistance -ISR).
hur ser signaleringen ut?
Signalling differs for various forms of induced resistance
Priming of plant defense to insect pests
beneficial insekts
herbivores - growth promation induced resistance
benificial microbes - nutrient allocation, plant defence, root exudates
Volatile signaling in plant defense and growth
Attacked plants can activate neighbours
Volatile compounds- Volatile Organic Compounds (VOC)
Methyljasmonate (MJ) – insect attack
Methylsalicylate (MS) – pathogen attack
PGPR can release VOCs that stimulate plant growth and defense
VOC
Volatile Organic Compounds
vad can genomics hjälpa till med
helpful for studies of biocontrol strains and action!?
Prediction of useful PGPR/BCA strains?
Secondary metabolites – yes!
Prediction of PGPR/BCA and relative efficacy!
Mechanisms by which microbes promote growth promotion and health of plants!
Bacterial rhizosphere competence – flagellum and chemotaxis. Plant growth–promoting traits e.g.: ACC deaminase (lowering ethylene), auxin (IAA) biosynthesis, biological nitrogen fixation, volatile organic compounds (VOC), phosphorus solubilization, siderophore production, …. Competition traits ISR possibility Resource allocation: abiotic stress tolerance
Breeding or priming for abiotic/biotic stress management?
Common pathways/factors for multiple stressors can be used as ”targets”.
Rapid test if microbes increase root system growth - exempel
For example Bacillus 5113 stimulates lateral root and root hair formation.
Increased phytohormone activity.
Indirect effect (ISR) to pathogens by root treatment with Bacillus 5113
Are plant associated microbes endophytic or epiphytic?
Common methods for detecting endophytes within a plant.
Desirable properties (as for natural enemies):
Good searching ability for host ”Host” specificity Reproduction rate Adaptability Host synchrony - well adapted to different stages of life cycle of target host Sustainability Ecosafe
Biocontrol agents – challenges in field conditions!?
Phyllosphere challenges for biocontrol microbes
Rhizosphere microbiota is affected by agriculture & environment
exempel?
plant species soil types agricultural practise climat plant diversety biotic interaktion
Is a PGPR always beneficial?
no - kan orsaka damage
applications - se pp
jupp - för myclet målande bilder
application natural field vs agricultural
Natural High diversity of plants Differential display of roots Diversified composition of exudates Deposition of heterogeneous organic matter Higher microbial diversity Effective selection of plants Plants rely on microbial partners for nutritional supply and protection
agricultural
Low diversity of plants (or even monoculture)
Homogeneous display of roots
Homogeneous release of exudates
Deposition of homogeneous organic matter
Lower microbial diversity
Defective selection of plants
Higher demand of human interference for plant
nutrition and protection
How important are shifts in natural plant microbiomes? Dynamics?
diverse: health
dysbiosis: disease
Spelar stor roll för hälsan - pp
Crop protection strategies
Chemical control Resistance breeding Semiochemicals Natural enemies PGPR/BCA – priming Unknown plant defence factors? Cultivation systems
SUMMARY
Many beneficial microbes exist in nature.
Microbiomes are complex and depend on several factors.
PGPR and BCA have great potential if low fitness cost for plants.
PGPR and BCA must have good rhizosphere competence.
PGPR and BCA must establish efficiently on roots (leaves).
PGPR and BCA must not trigger plant defense PRR-MAMP…
Priming-IST improve abiotic stress tolerance.
Priming-ISR unique signalling that sensitize innate immunity defense to pathogens.
Useful strategy as part of IPM.
Tools for designing/predicting productive beneficial interaction
Unexplored ecosystem service with great potential
Knowledge gaps
What are the requirements for succesful colonization, priming, ISR?
How predict efficacy ? (field conditions!!)
Can pests develop resistance to primed immunity?
Ecological effects of BCA?
Effects on other crops in crop rotation? Effects on neighbouring habitats?
Can weeds benefit from colonization and become more problematic?
Goal: Design future durable crop plant production
- Discuss some knowledge gaps that exist (and should be dealt with) in order to get more efficient pest control strategies!
- What risks with large scale use of PGPR/BCA may need more attention?
- Should resurce allocation strategies be more engineered in
crop plants?
allmänt
olika rötter - olika microber
Många av de plantorna vi är intresserade av är relativt nya
Plants kan ej flytta på sig och måste därmed lägga mer krut på defence
Ju further from root the lesser bacteria due to small in nr - outcompeated om för långt bort ifrån roten
Are okant microbes sopecies specific
Yes they are
Plant specific and plant specific - flytta till ett annat område och se hur adoptiv plantan och dess microber är
OUT - operational taxonomic unit - cluster of microbes with similar dna sequense
How is the microbion formed
Beror på soil type - vilka mo finns tillgängligt - beror lite på vilka plantor som växte där innan
Gradianter in the soil - fytokemikalier, orkaniska stuff
Plant genotype - hur ser cellväggarna ut
Hur vet mo långt bort I från plantan att plantan är där? Kan va random eller rootexudates - extremt viktigt för den här processen - shape the microbiome
Get rid of patogens, mycket secondära mecobolites - deliviring sugers eller liknande in the soil
Upp to 4% av fotosyntetic carbon is exodated - det över - är mycket = är viktigt
Många av de beneficial har flagella så kan röra sig mot plantan - följer gradienten
Qurorum sensing - känner hur många de är - om de är för få kanske de inte agerar men om de är tillräckligt många they act
10¨^7 cfu/ml brukar vara det som behövs
Under 10^5 så förlorar man effekten
Varför kan vissa mo var svåra att få att etablera sig
hur löser man det
Cultivate on plates
- vissa gillar ej agr - growth conditions - svårt at få till rätt miljö tex syrenicå - visa mo behöver andra microber för att fortsätta växa - gör andra saker på agarplattan än vad de skulle gra I jorden - endast 10% kan tas fram på det här sättet Meta genomics är vanligare - seqvensera den - utifrpn detta bestämma microdome
Problem med Biopesticel
Biopesticel - dyrt och time consuming så lättare att registrera det som en phytostimulator - säger att de kan stimulera tillväxt men inte tt det är bra för växten
Vad är priming
Betyder lite olika saker i olika situationer
Priming gör så att växten snabbare reagerar på threats och kan snabbare komma tillbaka till “sitt vanliga”
Why not maximal growth and defence for plants
Varför producerar ej plant mer growth hormones så växer mer
Do not really know
Kan växa mer men väljer att ej göra det
Blir en risk istället?
How do MAMP become accepted by plans
Other kind of signaling - vänlig signal -
Specific sensorer - fetaures on surface hos bra bakterier
Andra signl substanser
Posetiv receptor Produce some kind of hinhibitor that block reseprot Stör den inre signaling I växten - stops signaling steps eller transkription factoring But we do not really know
Hur kan man få växten att växa snabbare med hjälp av allt detta?
Cytokinin - fytokemikal som stimulerar växten att växa
Bakterier på roots som producerar vitiole som känns igen av löven
Många olika mekanismer som kan användas för att påverka växten
SAR?
det som produceras gör att insekten inte kan digest the plants
Votile signaling
Plants signalerar varandra - defens I den nya plant är redan aktiv när insekten kommer dit
Men sabbar ej the plants normal signaling
fint i pp
Endophytic or epip
Tools som avgör detta
- Pcr in real life
- Reisoloate - kan vara lite tricky
- Label microbes - microscope/ scan the plants
- Fish/pcr - veta den exakta dna sequensen
Alla dessa har sina posetiva sitor och sina negativa
vad spelar det för roll om det är en gammal eller ung planta
olika microber beroende på ung gammal planta
Bökig föreläsning och har ej mycket antekningar att gå på
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