Pierre Hohmann

Human limits in machine learning: prediction of potato yield and disease using soil microbiome data - BMC Bioinformatics Background The preservation of soil health is a critical challenge in the 21st century due to its significant impact on agriculture, human health, and biodiversity. We provide one of the first compreh...

This week’s AI in Agriculture 🌱

📊 A recent ML study shows soil microbiome data alone poorly predict yield and disease.

💡 Signal appears mainly when combined with soil & environmental variables.

✅ Microbiomes amplify context, not replace it.

🔗 link.springer.com/article/10.1...

Postdoc position in machine learning models for soil health prediction The Agrobiology and Soil Management Group (University of Barcelona) invites applications for a 12-month postdoctoral position (part-time, 0.5 FTE) focused on developing and validating machine learning...

Please share one last time!

📢 We’re hiring a #PostDoc @ub.edu!
❗Deadline's coming up: Nov 24

Join us to model soil health using ML of microbiome data. Join a creative team working towards sustainable ag & spin-off innovation 🚀

📅: Jan 2026
📍: Barcelona, Spain
🔗: euraxess.ec.europa.eu/jobs/383350

Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants - Nature Microbiology Metagenomes from prairie soils in Kansas, USA, show how historical exposure to water stress impacts soil microorganisms and subsequently drought responses in plants.

This week's special hot take!

💡 Microbes from dry-history soils boosted grass drought tolerance proving that soil microbiomes hold “climate memory”.

✅ Managing these legacies could aid crop resilience.

🔗 www.nature.com/articles/s41...

🔹 Culinary training and research in collective catering (1:15 p.m.)

With Dr. Marina Pérez Llorca, who will discuss how education and research drive innovation in this field.

ℹ️ https://tuit.cat/Veuwz

Soil monitoring: Parliament adopts new EU law with better support for farmers | News | European Parliament The new law will ensure soil is monitored in all EU countries and farmers get better support to improve soil health and soil resilience.

A big day for European Soils www.europarl.europa.eu/news/en/pres... #SoilHealth

Check out the latest EU CAP Network #EIPAGRI newsletter featuring an interview I had with Daniel Suter, Head of Forage Crop Variety Testing @agroscope.bsky.social:

sh1.sendinblue.com/15d9jpnd39tx...

We elaborate how variety testing can boost species mixtures in #plantbreeding and farming.

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...

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....

Postdoc position in machine learning models for soil health prediction The Agrobiology and Soil Management Group (University of Barcelona) invites applications for a 12-month postdoctoral position (part-time, 0.5 FTE) focused on developing and validating machine learning...

📢 We’re hiring! Pls help spread the word.

Postdoc (50%, 12 months) @ub.edu in Barcelona to model soil health using ML of microbiome data. Join a creative team working towards sustainable ag & spin-off innovation 🚀

Start: Jan 2026

🔗 euraxess.ec.europa.eu/jobs/383350

#PostDoc #JobsInAcademia

Harnessing artificial intelligence to decode the rhizosphere microbiome The rhizosphere microbiome plays crucial roles in plant health by regulating nutrient cycling and enhancing stress resilience. However, due to its com…

This week’s “AI in Agriculture” 🌱

📊 ML framework tackled microbiome data limits (dimensionality, compositionality, sparsity).

⚙️ Prospect: inside-out (hologenome breeding) + outside-in (SynCom design) + federated learning.

🔗 www.sciencedirect.com/science/arti...

#AIinAg

Exploring crop health and its associations with fungal soil microbiome composition using machine learning applied to remote sensing data - Communications Earth & Environment Crop health is improved by abundance of beneficial soil fungal genera and reduced by abundance of soil fungal pathogens, according to analysis of satellite-derived normalized difference vegetation ind...

This week’s “AI in Agriculture” 🌱

📊 ML corrected NDVI for abiotic factors, then linked residuals to fungal microbiomes.

✅ Promising route to soil-microbiome early-warning systems.

🔗 doi.org/10.1038/s432...

#AIinAg #Microbiome #SoilHealth

A study of Universal ODE approaches to predicting soil organic carbon Soil Organic Carbon (SOC) is a foundation of soil health and global climate resilience, yet its prediction remains difficult because of intricate physical, chemical, and biological processes. In this ...

This week’s “AI in Agriculture” 🌱

📊 Universal ODE hybrid model predicted SOC change with R² ≈ 0.9999 in low-noise tests, with moisture, temperature & microbial turnover as key drivers.

⚠️ Sensitive to noisy data → needs uncertainty-aware training.

🔗 arxiv.org/abs/2509.24306

#AIinAg #SoilCarbon

Professor or Assistant / Associate (tenure track) Professor in Plant Ecology The Faculty of Science is looking for a full professor or assistant/associate professor (tenure track) in Plant Ecology. The aim of the professorship is to strengthen scientific research and education...

Open position: Professor or Assistant / Associate (tenure track) Professor in Plant Ecology (U. Turku Finland) Please share

ats.talentadore.com/apply/kasvie...

AgroLLM: Connecting Farmers and Agricultural Practices through Large Language Models for Enhanced Knowledge Transfer and Practical Application AgroLLM is an AI-powered chatbot designed to enhance knowledge-sharing and education in agriculture using Large Language Models (LLMs) and a Retrieval-Augmented Generation (RAG) framework. By using a ...

This week’s “AI in Agriculture” 🌱

📊 AgroLLM benchmarked LLMs with RAG on agri corpora → ChatGPT-4o Mini reached 93% accuracy, better than Gemini & Mistral

✅ Specialised LLMs may be a future of ag knowledge transfer

🔗 arxiv.org/abs/2503.04788

#AIinAg #LLM #RAG

📢 PhD opening in Barcelona! Join our group.

Research soil health and carbon cycling. Recent grad (2021-25) w/ > 8.5 grade & R/Python skills.

Details: www.linkedin.com/posts/agrobi...

#PhDJobs #AcademicJobs #PhDPosition

Microbiome-driven machine learning for predicting suppressiveness to Rhizoctonia solani in organic-amended soils This study introduces a microbiome-integrated machine learning framework to predict soil suppressiveness against Rhizoctonia solani, a destructive fun…

This week's "AI in Agriculture" 🌱

📊 Soil microbiome profiles analysed with random forest models predicted whether soils suppress Rhizoctonia solani

✅ Promising step towards microbiome-informed tools for soil health and biocontrol

www.sciencedirect.com/science/arti...

#AIinAg #Microbiome

Blueprints for sustainable plant production through the utilization of crop wild relatives and their microbiomes - Nature Communications Authors discuss the potential of conserving crop wild relatives, together with the associated communities of microorganisms, to unlock strategies for improving crop resilience and achieving food secur...

This week's "AI/ML in Agriculture" hot take: www.nature.com/articles/s41...

💡CWRs host microbes modern crops lost → relevant for resilience traits. ML helps model which pairings matter most.

✅ Fits with our @cousinproject.bsky.social, where we aim for microbiome-mediated trait transfers

📢Oportunidad predoctoral en Barcelona: Investigación sobre efectos de la tinta de tatuajes durante su proceso de eliminación✒

🎓Perfil:
Graduado en Nutrición, Enfermería, Biología, Química, Farmacia o Medicina
✅Graduado entre 2021-25
✅Nota media > 8.5
✅Conocimientos Estadística (Stata/R)

Glad to be part of this team calling on global scientific and conservation communities to get on board to protect microbial life, which sustains all forms of life on our planet.

in @natmicrobiol.nature.com

www.nature.com/articles/s41...

Roots: metabolic architects of beneficial microbiome assembly Abstract. The increasing demand for sustainable agricultural practices has driven a renewed interest in plant–microbiome interactions as a basis for the ne

🔬🌱Our review “Roots: metabolic architects of beneficial microbiome assembly” led by PhD candidate Melissa Uribe Acosta @plantphys.bsky.social discusses plant mechanisms of root microbiome selection. Co-authors: @cornepieterse.bsky.social Jiayu Zhou Alberto Pascale.
academic.oup.com/plphys/artic...

Exploring crop health and its associations with fungal soil microbiome composition using machine learning applied to remote sensing data - Communications Earth & Environment Crop health is improved by abundance of beneficial soil fungal genera and reduced by abundance of soil fungal pathogens, according to analysis of satellite-derived normalized difference vegetation ind...

AI/ML in Agriculture - This week’s hot take 🌱

📊 Satellite crop health signals linked to soil fungal microbiomes
💡 Associations appear after adjusting for weather and soil
⚠️ For now: associations not causation
✅ Satellites guide, fungi explain!

🔗 www.nature.com/articles/s43...

#AIinAg #Microbiome

There's a lot happening in AI, and we made a way to keep up.

@genomelybio.bsky.social will now post weekly reports about AI (& beyond). Eg, we examined & summarized 166 articles, 56 community posts (eg, from Reddit), and 10 trending topics (eg, from Bluesky)

genomely.substack.com/p/ai-weekly-...

Explore related resources from the Focus Group on crop associations on eu-cap-network.ec.europa.eu/focus-group-...

Breeding for species mixtures: 50 Years, One Key Metric - Exporting Switzerland's Competitive-Ability Approach from Pasture to Arable Systems? Crop associations (CAs), the cultivation of multiple crop species together as intercrops, offer significant benefits for sustainable agriculture. However, a major bottleneck for broader adoption is the lack of CA-oriented cultivar testing and breeding.For more than fifty years in Switzerland, varieties have undergone testing not only in pure but also in mixed stands, and thus provided a rare example of integrating CAs in an official variety testing scheme. The primary objective is to gain insights into the competitive strength of the tested varieties. This information holds particular significance in the formulation of clover-grass mixtures, as over 90% of cultivated fields in Switzerland, dedicated to meadows and pastures, have traditionally been sown with clover-grass mixtures. This longstanding practice reflects the agricultural importance attached to understanding the interplay between different varieties in mixed cropping systems. As part of a mini paper on “Cultivar testing as a key to boost uptake of crop associations in breeding and farming” (see related EU CAP Focus Group output at https://eu-cap-network.ec.europa.eu/focus-group-crop-associations-including-milpa-and-protein-crops_en), an interview with Dr. Daniel Suter, Head of Variety Testing for Forage Crops in Switzerland, delved into the intricacies of forage crop variety testing and its implications for agricultural practices and breeding strategies. The purpose of this interview is to provide valuable information that might help to transfer this successful application of CA cultivar testing to forage crop testing schemes in other countries and possibly extrapolate insights to other cultivation systems such as arable farming.

How can mixing ability be integrated into variety testing?

An interview with Dr. Daniel Suter, Head of Forage Crop Variety Testing @agroscope.bsky.social offers lessons for other countries and cropping systems.

Published now open-access at:
zenodo.org/records/1707...

The discovery of genes underlying interesting traits for #PlantBreeding is one of the most important & difficult tasks here @kwsgroup.bsky.social.

We are looking for a Quantitative Geneticist to help us with this!

#PlantScience #PlantBreeding #PlantGenetics #PlantScienceJobs #PlantSciJobs

3 Post doc positions in biodiversity science, genetic indicator assessment and ecological statistics 3 Post doc positions in biodiversity science, genetic indicator assessment and ecological statistics

📢 Post doc! Want to join our team?

We are looking for 3 post docs in biodiversity science, genetic indicator assessment, and ecological statistics for a fixed term of 2 years!

Come unravel the drivers and consequences of global change on biodiversity with us!

DL 24.9.
#universityofhelsinki

Failure & misfortune… and one more Horizon.

Past year summary: 5 big proposals. All rejected. I know the odds are low. But it still feels brutal. So much effort, then nothing.

Today, I hit submit on yet another Horizon. On my birthday. Feels symbolic. Another step forward… or not. 😬

OpenAI just launched “OpenAI for Science” 👉 threadreaderapp.com/thread/19629...
Cool idea: AI as a real scientific instrument.
But… hallucinations are still a thing.
Makes me wonder what this means once ag data and models get fed in. 🤔
Might have big implications for farmer decision support tools. 🚜

This study is the result of many years of unwavering dedication of several key people around Michael Schneider and @monikamessmer.bsky.social. It marks an important step toward making #microbiome based resistance #breeding a reality.

bmcplantbiol.biomedcentral.com/articles/10....