The inherited microbiome of oak

Ahmed AbdelfattahPostdoctoral Fellow

Department of Ecology,

Environment and Plant Sciences

Stockholm University

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The Fruit Microbiome: A New Frontier

Plants, with no exception thus far, are

associated with an abundant collection of

microbes.

The tissues of healthy plants are sterile (Pasteur 1876).

1876 Pasteur

Louis Pasteur 1882 -1895

Marie Louis Victor Galippe (1848-1922). A pioneer on microbes colonizing plants and their soil origin.

1887 Galippe

• Isolated bacteria from various plants parts.

• He suggested that those microbes originate from the soil.

Hermann Hellriegel(1831-1895)

Hermann Wilfarth(1853-1904)

1888 Hellriegel and Wilfarth

The first indication of microbial endophytism.

Discovered the symbiotic association between Nitrogen fixing bacteria and legumes.

Hellriegel and Wilfarth “divided-root experiment” with pea plants.

Lorenz Hiltner (1862- 1923), Soil Bacteriologist and Professor of Agronomy at the Technical College of Munich, coined the term "rhizosphere" and emphasized the critical role of microbial activities in this root zone in relation to the nutrition and general health of plants

• Coined the term rhizosphere to describe the area in close proximity to the plant roots which interactions between bacteria and legumes roots occurs the most

• He also suggested that the quality of plant productsmay be dependent on the composition of the root microflora

1904 Hiltner

1956 Jakoba Ruinen

Carl Richard Woese1928-2012

DNA sequencing timeline and milestones

Frederick Sanger 1918-2013

Kary Mullis 1944-2019

Timeline showing advances in microbial communities studies from Leeuwenhoek to NGS

(Ottman et al., 2012; Yarza et al., 2014).

Induce resistance

Production of pathogen inhibitory compounds

Growth +

Water availability

• Growth promoters e.g. (Cytokinin and Gibberellins)

• Carbon, nitrogen, and phosphorus fixation

• Disease tolerance through induced resistance or by producing inhibitory compounds

• Tolerance to abiotic stresses • Drought: Increasing water availability • Cold: heat production• Detoxification• UV tolerance (Pseudomonas biofilm)

The plant microbiome

Hots genotype

Species 1Species 1

Species 2Species 2

Correlation between plant phylogeny and microbial community composition.

e.g. PCA

Hots genotype is one of the main determinants of the microbial community composition.

Is soil the source of all plant microbes?

Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies (Gopal and Gupta 2016)

Can seed help the continuity of the plant microbes?

Studies on seed microbial community Plant References

Herbaceous and woody species Mundt and Hinkle 1976Soybean Kremer 1987Broadleaf weed species Kremer 1987Maize Dunleavy 1989Bean Pleban et al. 1995Cauliflower Pleban et al. 1995Wild mustard Pleban et al. 1995Rice Mukhopadhyay et al. 1996Rapeseed Granér et al. 2003Wheat Coombs and Franco 2003Sugar beet Dent et al. 2004Norway spruce Cankar et al. 2005Coffee Vega et al. 2005Garden pea Smerda et al. 2005

Strawberry Kukkurainen et al. 2005Grasses Ikeda et al. 2006Eucalyptus Ferreira et al. 2008Tobacco Mastretta et al. 2009Cactus Puente et al. 2009Ash Donnarumma et al. 2010Grape vine Compant et al. 2011Pumpkin Fürnkranz et al. 2012Peanut Sobolev et al. 2013Thale cress Truyens et al. 2013Tomato Xu et al. 2014

Hologenome(1) All animals and plants establish

symbiotic relationships with microorganisms.

(2) Symbiotic microorganisms are transmitted between generations.

(3) The association between host and symbionts affects the fitness of the holobiont within its environment.

(4) Changing either the host genome or the microbiome results in variations in

the holobionts .

1- This principle was based on the obligate or extreme symbionts (Mitochondria, Chloroplast, Wolbachia, Mycorrhiza)

2- Until now, there is no actual evidence for inheritance in plants.

(Ilana Zilber-Rosenberg & Eugene Rosenberg 2008)The holobiont (host with its endocellular and extracellular microbiome) can function as a distinct biological entity.

Hologenome theory of evolution

Main findings • Most seeds contain one species of fungus• Pollen endophytes can be transmitted to

ripe seeds and leaves

Limitations1- The work was based on PDA-isolation 2- Roots were not analyzed

Limitations 1- Used Terminal-Restriction Fragment Length Polymorphism (T-RFLP)2- They used seeds from seed bank and didn’t track their transmission to offspring (seedlings)

Main findings1- Substantial contributions of both or either parent in the shaping of the bacterial seed endophytes of the offspring.

Parent

Hybrid

Limitations1- A clonal plant was used as plant model2- The experiment was carried out in a greenhouse

Ground-ivy

Main findingsA significant proportion of the mother microbial community is transmitted to the daughters

To prove microbial inheritance (in theory) we need:

• Mature Seed, endophytes, preferably embryonic• Eliminate the risk of contamination from the

surrounding environment• Avoid seeds that had contact with soil • Harsh surface sterilization• Grow plants in sterile soil (substrate)• Grow plants in sterile air• Avoid above- and below-ground cross talk

40 Acorns 40 Acorns Planted in microcosms

Surface-sterilized acorns8% NaClO 30 min.

Pericarps Embryos

ITS rDNAIllumina MiSeq V3

Amplicon sequencing

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

Embryo Pericarp Root Leaf

Rel

ativ

e ab

un

dan

ce %

Most abundant fungal phyla

Ascomycota Basidiomycota unidentified

0.0000%

0.0005%

0.0010%

0.0015%

0.0020%

0.0025%

0.0030%

0.0035%

Embryo Pericarp Root Leaf

Rel

ativ

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un

dan

ce %

Rare phyla

Glomeromycota Mucoromycota

• Glomus, an arbuscular mycorrhiza fungi (AMF) in embryos and roots

• Embryos were dominated by Basidiomycetes

• While they were absent in pericarps

Main findings

LeavesEmbryo Roots Pericarps

Leaves

Embryo

Roots

Pericarps

Main findings

• Leave resembled the fungal community of embryo in both structure and composition

• Roots and pericarps seemed to have a distinct community.

PCoA plot of Beta diversity (Bray Curtis index)

• Most abundant taxa were shaped between all samples

• No bottleneck effect is clear• Unique taxa were in embryos and

pericarps • Unique taxa in leaves and roots?

Main findings

32%

6%

33%

27%

• Pericarp contributed equally to roots and phyllosphere community

• Embryo had very little contribution to the roots

• Explains why embryos and leave had a similar community

Remarks

• Seed microbiome represents the source and initial microbiota to the plant root and phyllosphere

• Studying seed microbiome can provide an explanation for the genotype effect and the continuity of the plant microbiome

• The presence/absence and identity of the primary symbiont in each seed affects the survival of the host in the vulnerable stages of seed dispersal, germination, emergence and young growth (Primary Symbiont Hypothesis)

• Maternal transmission is universal in kingdom animalia but it has to be yet proved in plant

• While our understanding of the seed microbiota has lagged far behind that of the rhizosphere and phyllosphere, many advances are now being made

Remarks

The origin, distribution, and dissemination of the apple microbiome

Apple-Biome

https://applebiome.com/

Questions?

Thank you for you attention!

Contact me at ahmed.abdelfattah@su.se

Follow me at @AhmedAb60567245

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