The Leaf Microbiome of
            <i>Arabidopsis</i>
            Displays Reproducible Dynamics and Patterns throughout the Growing Season

Almario, Juliana; Mahmoudi, Maryam; Kroll, Samuel; Agler, Mathew; Placzek, Aleksandra; Mari, Alfredo; Kemen, Eric

doi:10.1128/mbio.02825-21

Cited by 27 publications

(33 citation statements)

References 55 publications

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“…These strains were selected based on a pre-screen which revealed gram-positive bacteria to be more sensitive to the protein treatment than gram-negative. The microbial collection also includes strains that were detected as core members in the A. thaliana phyllosphere microbiome, meaning they are consistently present in natural communities and hence are likely to inhabit the plant before or during an Albugo infection (Almario et al, 2022). Overall, we observed a variable effect on the growth of bacteria, with species within the same genus showing different responses.…”

Section: Resultsmentioning

confidence: 99%

“…The dataset combined analyses of 16S and 18S ribosomal RNA phylogenetic marker genes as well as of the ITS regions. We analyzed the raw OTU tables (Mahmoudi et. al, 2022, in preparation) that were constructed after a 97% similarity OTU clustering, using the software FlashWeave with a 0.05 significance cutoff, controlling for confounding meta variables including season, year, sampling site and phyllosphere compartment (Tackmann et al, 2019).…”

Section: Methodsmentioning

confidence: 99%

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Proteins released into the plant apoplast by the obligate parasitic protist Albugo selectively repress phyllosphere-associated bacteria

Gómez-Pérez

Schmid

Chaudhry

et al. 2022

Preprint

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Biotic and abiotic interactions shape natural microbial communities. The mechanisms behind microbe-microbe interactions, particularly those protein-based, are not well understood. We hypothesize that secreted proteins are a powerful and highly specific toolset to shape and defend plant niches. We have studied Albugo candida, an obligate plant parasite from the protist Oomycota phylum, for its potential to modulate the growth of bacteria through secretion of proteins into the apoplast. Amplicon sequencing and network analysis of Albugo-infected and uninfected samples revealed an abundance of negative correlations between Albugo and other phyllosphere microbes. Analysis of the apoplastic proteome of Albugo colonized leaves combined with machine-learning predictors enabled the selection of candidates for heterologous expression and study of their inhibitory activity. We found that three of the candidate proteins show selective antimicrobial activity on gram-positive bacteria isolated from Arabidopsis thaliana and that these inhibited bacteria are important for the stability of the community structure. We could ascribe the antibacterial activity of the candidates to intrinsically disordered regions and positively correlate it with net charge. This is the first report of protist proteins with antimicrobial activity under apoplastic conditions that therefore are potential biocontrol tools for targeted manipulations of the microbiome.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Proteins released into the plant apoplast by the obligate parasitic protist Albugo selectively repress phyllosphere-associated bacteria

Gómez-Pérez

Schmid

Chaudhry

et al. 2022

Preprint

Self Cite

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“…Fungi from the Capnoideales and Hypocreales are among the top 10 in relative abundance across all three sites, but this is not the case for Polypropales. The Hypocreales and Capnodiales were core members of the microbiome of Arabis alpina root (Almario et al, 2017) and Arabidopsis thaliana leaves (Almario et al, 2022) respectively. Tremellales, Helotales, and Pleosporales are also orders which show conserved high relative abundance orders across terrestrial plants and duckweed.…”

Section: Bmentioning

confidence: 99%

Pseudomonasisolates from ponds populated with duckweed prevent disease caused by pathogenicPseudomonasspecies

Baggs

Stark

Tiersma

et al. 2022

Preprint

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Duckweeds are notoriously invasive plants. They are successful in inhabiting diverse environments, despite their lack of conventional immune pathways that are essential for disease resistance in other plant species. It is unclear how duckweeds thrive in the absence of these immune pathways. In this study, we investigated the effect of bacteria from duckweeds natural habitat on disease progression utilizing the duckweed-Pseudomonas pathosystem. Through nanopore sequencing of 16S and ITS rDNA amplicons we identified duckweed-associated bacterial and fungal genera present at three environmental sites. The pond filtrate from one of the three environmental locations primed duckweeds pathogen defenses leading to a reduction in disease symptoms. Furthermore, we were able to identify bacterial isolates from the filtrate that protect duckweed from disease symptoms upon Pseudomonas pathogen inoculation. The isolated protective bacteria belong to the Pseudomonas genus and we demonstrated antagonistic interactions between the pathogen and beneficial strains in vitro and in vivo. The ability of our environmental isolates to protect against Pseudomonas pathogens appears to be plant/species specific as environmental strains showed no protective effect against Pseudomonas pathogens in Arabidopsis assays. Genome sequencing of the beneficial Pseudomonas strains showed the presence of several genes involved in bacterial competition. We have thus demonstrated that Pseudomonas species from duckweeds natural habitat can successfully antagonize other plant pathogens.

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“…Among these outcomes, the concept of core microbiota has been stablished for Arabidopsis, showing that it harbors community members that are essentially constant [ 30 , 115 , 169 ], while others are variably affected by the soil type, ecotype, developmental stage [ 115 ], season [ 3 , 15 , 30 ], generation [ 183 ], and other factors playing minor contributions (Fig. 2 A).…”

Section: Introductionmentioning

confidence: 99%

The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant–microbe interactions

Poupin

Ledger

Roselló-Móra

et al. 2023

Environmental Microbiome

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As holobiont, a plant is intrinsically connected to its microbiomes. However, some characteristics of these microbiomes, such as their taxonomic composition, biological and evolutionary role, and especially the drivers that shape them, are not entirely elucidated. Reports on the microbiota of Arabidopsis thaliana first appeared more than ten years ago. However, there is still a lack of a comprehensive understanding of the vast amount of information that has been generated using this holobiont. The main goal of this review was to perform an in-depth, exhaustive, and systematic analysis of the literature regarding the Arabidopsis–microbiome interaction. A core microbiota was identified as composed of a few bacterial and non-bacterial taxa. The soil (and, to a lesser degree, air) were detected as primary microorganism sources. From the plant perspective, the species, ecotype, circadian cycle, developmental stage, environmental responses, and the exudation of metabolites were crucial factors shaping the plant–microbe interaction. From the microbial perspective, the microbe-microbe interactions, the type of microorganisms belonging to the microbiota (i.e., beneficial or detrimental), and the microbial metabolic responses were also key drivers. The underlying mechanisms are just beginning to be unveiled, but relevant future research needs were identified. Thus, this review provides valuable information and novel analyses that will shed light to deepen our understanding of this plant holobiont and its interaction with the environment.

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The Leaf Microbiome of Arabidopsis Displays Reproducible Dynamics and Patterns throughout the Growing Season

Cited by 27 publications

References 55 publications

Proteins released into the plant apoplast by the obligate parasitic protist Albugo selectively repress phyllosphere-associated bacteria

Proteins released into the plant apoplast by the obligate parasitic protist Albugo selectively repress phyllosphere-associated bacteria

Pseudomonasisolates from ponds populated with duckweed prevent disease caused by pathogenicPseudomonasspecies

The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant–microbe interactions

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