Marie Simonin
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microbialmarie.bsky.social
Marie Simonin
@microbialmarie.bsky.social
860 followers 560 following 25 posts
Ecologist studying plant microbiota assembly and microbiome engineering / Seeds / SynComs 🦠/ Sustainable agriculture 🌾
Researcher at INRAE, France
http://mariesimonin.com/
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microbialmarie.bsky.social
Marie Simonin @microbialmarie.bsky.social · Sep 12
Happy to see our paper out in Current Op in Microbiology!
We show how transient microbes can play key roles in plant fitness & microbiota assembly 🦠
The 1st 1st author article for my 2 fantastic PhD students @logansuteau.bsky.social & Louna Coleart-Sentenac 🎉
www.sciencedirect.com/science/arti...
www.sciencedirect.com
Reposted by Marie Simonin
nemopeeters.bsky.social
Excited to bring to your attention 2-year work by @sylvain-vicente.bsky.social and collaborators #BIOSP #MathNum @inrae-dpt-spe.bsky.social. A re-evaluation of STAMP modelling, introducing a much needed time-resolution. Works also on Animal-bacterial infection models. www.biorxiv.org/content/10.1...
November 23, 2025 at 5:34 PM
Reposted by Marie Simonin
rlberendsen.bsky.social
🎉 Check out the latest from Qin Gu’s team at Nanjing Agricultural University: “Keystone Pseudomonas species in the wheat phyllosphere” (Cell Host & Microbe) 👉 www.cell.com/cell-host-mi...
Keystone Pseudomonas species in the wheat phyllosphere microbiome mitigate Fusarium head blight by altering host pH
Fusarium graminearum (F. graminearum) pathogen induces wheat phyllosphere alkalinization, promoting the development of Fusarium head blight (FHB). Xu et al. show that host-acidifying Pseudomonas, sele...
www.cell.com
November 23, 2025 at 8:11 AM
Reposted by Marie Simonin
thomaslenormand.bsky.social
Un poste d’IE en bioinformatique est actuellement ouvert au CEFE à Montpellier pour travailler dans le cadre de l'ERC RegEvol.

Détails ici:

emploi.cnrs.fr/Offres/CDD/U...

Début 01/01/2026 pour 18 mois potentiellement renouvelable.

candidature jusqu'au 29/11

N’hésitez pas à diffuser largement
Portail Emploi CNRS - Offre d'emploi - Ingénieur d'études en bioinformatique (H/F)
emploi.cnrs.fr
November 18, 2025 at 3:09 PM
Reposted by Marie Simonin
aabdelfattah.bsky.social
New work in @newphyt.bsky.social: fruit isn’t not only for #seed dispersal, it filters and redirects #microbiome assembly in the next plant generation. This should change how we think about inheritance beyond #seeds.

nph.onlinelibrary.wiley.com/doi/10.1111/...
Impact of fruit decomposition on soil and plant microbiomes. (a) Fruits harbor their own microbiome, which is released into the soil upon decomposition. (b) Fruit decomposition changes the soil microbiome by introducing fruit-associated microbes and altering microbial interactions. (c) As seeds germinate, the enriched soil microbiome colonizes the emerging plant, influencing the microbial assembly in roots and shoots. This interplay between fruit decomposition, soil microbial dynamics, and plant colonization suggests that fruits may play an active role in shaping the microbiome of the next plant generation beyond seed dispersal. This figure was created in BioRender (https://BioRender.com/tw7zbn6).
November 17, 2025 at 8:13 PM
Reposted by Marie Simonin
fmartin54.bsky.social
We are delighted to let you know that your Plants, People, Planet article 'Demystifying Fungal Systematics: A Gateway to Fungal Literacy and Societal/Ecological Relevance Through Familiar Species' has been published on Early View.

nph.onlinelibrary.wiley.com/doi/10.1002/...
Demystifying fungal systematics: A gateway to fungal literacy and societal/ecological relevance through familiar species
Fungal systematics can feel overwhelming given the vast species diversity within this kingdom, with numerous subgroups at every taxonomic rank. This often creates a disconnect between the undertsnidn...
nph.onlinelibrary.wiley.com
November 14, 2025 at 5:05 PM
Reposted by Marie Simonin
labwaggoner.bsky.social
A gene-editing approach enables modification of bacteria within the mouse gut @science.org @harriswang.bsky.social @columbiauniversity.bsky.social @shsternberg.bsky.social
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
November 14, 2025 at 3:36 AM
Reposted by Marie Simonin
maggie-r-wagner.bsky.social
Long term deleterious effects of drought memory
buff.ly/0sNZeWs
A 5-year long experiment, super impressive! I wonder whether the offspring of the final generation would have retained the performance difference, esp. after controlling for seed size/maternal investment.
Transgenerational decline through insidious effects of drought memory
Click on the article title to read more.
buff.ly
November 11, 2025 at 7:15 PM
Reposted by Marie Simonin
sophiejwalton.bsky.social
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 11, 2025 at 5:15 PM
Reposted by Marie Simonin
sophiejwalton.bsky.social
However, these findings are consistent with recent ecological theory by my amazing labmate @johndmcenany.bsky.social which suggested that conspecific strains may coexist in saturated communities even when new strains displace other species. (15/n) www.nature.com/articles/s41...
Predicting the first steps of evolution in randomly assembled communities - Nature Communications
Evolution often occurs within complex communities, but the way this context controls the rate and impact of evolution is poorly understood. The authors employ a model of resource competition to study ...
www.nature.com
November 11, 2025 at 5:15 PM
Reposted by Marie Simonin
evolvedbiofilm.bsky.social
The hitchhiker’s guide to cross-species DNA delivery

@cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez

www.cell.com/trends/micro...
The hitchhiker’s guide to cross-species DNA delivery
Microbial hitchhikers are rewriting the rules of horizontal gene transfer. He, Patkowski, et al. reveal how phage satellites assemble chimeric infective particles that deliver DNA across species bound...
www.cell.com
November 9, 2025 at 9:39 AM
Reposted by Marie Simonin
evolvedbiofilm.bsky.social
Strain displacement in microbiomes via ecological competition

Cool @natmicrobiol.nature.com publication by @erikbakkeren.bsky.social
@vit-pi.bsky.social @meganleeny.bsky.social @microscape.bsky.social & Kevin Foster

www.nature.com/articles/s41...
Strain displacement in microbiomes via ecological competition - Nature Microbiology
Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.
www.nature.com
November 7, 2025 at 2:19 PM
microbialmarie.bsky.social
#PMS2025 Check the posters of my 2 wonderful PhD students @logansuteau.bsky.social & Louna Colaert-Sentenac!

Results on multi-kingdom SynCom experiments inoculated on seeds to perform plant microbiome engineering & promote pathogen resistance on rapeseed & common bean 🫘 🌱
@emersys-irhs.bsky.social
November 6, 2025 at 1:43 PM
microbialmarie.bsky.social
Come check my poster 137 "Seed Microbiota: Core diversity, Transmission and Legacy effects on Plant Microbiome Assembly"
Some results from the SUCSEED project on culturomics and SynComs 🫘🧫🌱 #PMS2025
@emersys-irhs.bsky.social
November 4, 2025 at 8:10 AM
microbialmarie.bsky.social
Very happy to be in Antequera, Spain for #PMS2025 with my 2 PhD students @logansuteau.bsky.social and Louna Coleart-Sentenac
We will present results from the SUCSEED project on culturomics and seed microbiome engineering using multi-kingdom SynComs 🫘🧫
@emersys-irhs.bsky.social
November 2, 2025 at 10:28 PM
Reposted by Marie Simonin
microsos.bsky.social
Final countdown before the start of the #PMS2025!!! 🪴

Looking forward to seeing you in Antequera (Malaga) on 3-7 November!
Final program at: 6thplantmicrobiomesymposium2025.com/programme/

#Plantscience #MicrobiomeResearch #Bioinformatics
October 30, 2025 at 6:03 PM
Reposted by Marie Simonin
luzia-stalder.bsky.social
Still using 16S/ITS profiling? You might want to reconsider👀

Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable!
microbiomejournal.biomedcentral.com/articles/10....
High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons - Microbiome
Background High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. Results...
microbiomejournal.biomedcentral.com
October 30, 2025 at 1:32 PM
Reposted by Marie Simonin
newphyt.bsky.social
Signatures of local nitrogen adaptation in the Brachypodium distachyon root microbiome

Ricks et al.

nph.onlinelibrary.wiley.com/doi/10.1111/...
Expectations for adaptive recruitment in the microbiome.
October 30, 2025 at 11:17 PM
Reposted by Marie Simonin
uncultured.carinilab.com
ICYMI: Our latest shows what happens to transcriptional and metabolic profiles in a desiccated soil bacterium.

To simplify things, I've attached a visual abstract.

Comments on the preprint are welcome!
#microsky #microbesky

www.biorxiv.org/content/10.1...
October 30, 2025 at 7:35 PM
Reposted by Marie Simonin
phytobiomesjournal.bsky.social
Léa Ninzatti, Marie-Françoise Jardinaud, and Aurélien Carlier review current knowledge of hereditary leaf symbiosis in tropical plants and explore hypotheses regarding mechanisms that enable these highly specific interactions: https://doi.org/10.1094/PBIOMES-11-24-0111-RVW
Fig. 1. Diversity of leaf symbiotic structures.
October 21, 2025 at 4:55 PM
Reposted by Marie Simonin
newphyt.bsky.social
Martin Zobel is the corresponding author of the recently published #TansleyReview ‘#Symbiont plasticity as a driver of plant success.’

📖 doi.org/10.1111/nph....

#mycorrhiza #PlantScience
Manifestation of symbiont plasticity, expressed as root mutualist flexibility.
October 17, 2025 at 5:09 PM
Reposted by Marie Simonin
prof-braj-singh.bsky.social
We are searching for a 4- year postdoctoral fellow to work us on Microbial Ecology and Crop Disease Management.

More details below. The position will start next year.

Please circulate and repost.

jobs.smartrecruiters.com/WesternSydne...
October 2, 2025 at 4:32 AM
Reposted by Marie Simonin
maddyseale.bsky.social
Wonderful to see this beautiful image on the cover of Science this week highlighting a paper that uses high resolution imaging to show the spatial patterns of bacterial attraction to glutamine from roots.
Paper here: www.science.org/doi/10.1126/...
Perspective here: www.science.org/doi/10.1126/...
October 7, 2025 at 9:52 AM
microbialmarie.bsky.social
Great night for the Fête de la Science at the stunning Digital Floralia exhibition (Miguel Chevalier)-Musée des Beaux Arts Angers
I enjoyed chatting about our research on seed microbiota, holobionts and alternatives to pesticides 🦠👩‍💻🌱
@emersys-irhs.bsky.social @irhs-angers.bsky.social
October 2, 2025 at 9:23 PM
Reposted by Marie Simonin
symbionticism.bsky.social
"Tick–pathogen–microbiome interactions based on #hologenome-wide analysis" from 16,000 ticks, 48 species, and 8 genera. 👀

Nutritional endosymbionts are prevalent with a new 7,783 bacterial genomes from 1,373 bacterial species. @holobiontbiology.bsky.social

www.nature.com/articles/s41...
Genome-resolved metagenomics reveals microbiome diversity across 48 tick species - Nature Microbiology
Sequencing the genome and microbiome of about 1,500 tick samples from regions across China revealed host–microbe associations in ticks that could have implications for controlling ticks and tick-borne diseases.
www.nature.com
September 29, 2025 at 7:14 PM
Reposted by Marie Simonin
tcahitch.bsky.social
The main work from my time in Aachen is now out 🎉 if you have wanted to make a SynCom that captures the functional-landscape of microbiota, MiMiC2 makes that possible based on metagenomic data! 1/7 doi.org/10.1093/isme...
Function-Based Selection of Synthetic Communities Enables Mechanistic Microbiome Studies
Abstract. Understanding the complex interactions between microbes and their environment requires robust model systems such as synthetic communities (SynCom
doi.org
September 24, 2025 at 1:22 PM