🆕 The new issue of Annals of Botany is now online!
🌱 How leaf-dwelling fungi can reshape soil chemistry
🌬️ Why some wind-pollinated plants evolved grass-like traits
🔥 How plants recover after fire, drought, and salinity
and more…
New issue👉 https://botany.fyi/bep8tb
#plantscience #botany #plantbiology #soilmicrobiome #plantfungi #pollinationbiology #windpollination
#plantecology #plantadaptation #stresstolerance #fireecology
This week’s AI in Agriculture 🌱
📖 Human limits in machine learning: prediction of potato yield and disease using soil microbiome data (BMC Bioinformatics, 2024: https://link.springer.com/article/10.1186/s12859-024-05977-2
💡 Soil microbiome data alone showed limited predictive power for yield and disease.
📊 ML performance improved mainly when soil, environmental and management variables were integrated, with careful preprocessing.
✅ Microbiomes act as context-aware amplifiers, not standalone predictors.
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 comprehensive investigations into the predictive potential of machine learning models for understanding the connections between soil and biological phenotypes. We investigate an integrative framework performing accurate machine learning-based prediction of plant performance from biological, chemical, and physical properties of the soil via two models: random forest and Bayesian neural network. Results Prediction improves when we add environmental features, such as soil properties and microbial density, along with microbiome data. Different preprocessing strategies show that human decisions significantly impact predictive performance. We show that the naive total sum scaling normalization that is commonly used in microbiome research is one of the optimal strategies to maximize predictive power. Also, we find that accurately defined labels are more important than normalization, taxonomic level, or model characteristics. ML performance is limited when humans can’t classify samples accurately. Lastly, we provide domain scientists via a full model selection decision tree to identify the human choices that optimize model prediction power. Conclusions Our study highlights the importance of incorporating diverse environmental features and careful data preprocessing in enhancing the predictive power of machine learning models for soil and biological phenotype connections. This approach can significantly contribute to advancing agricultural practices and soil health management.
Paper of the week - week 44 (this week):
Hartmann et al. 2015
Distinct soil microbial diversity under long-term organic and conventional farming
https://doi.org/10.1038/ismej.2014.210
#benediktspapersoftheweek #soilmicrobiome #FarmingPractices #OrganicConventional #OrganicFarming #Biodiversity #SoilManagement
Just was following an extremely interesting presentation of one of our group's PhD students' projects, titled:
“Mining of the rhizosphere microbiome for potato late blight resistance” by Lihong Yan.
I cannot share too much but very interesting results are to come, that will change the way we think about phytopathology and resistance breeding. I will share Lhong We really should work more interdiciplinarily in plant breeding (and agronomy in general). Plants arent isolated units in an ecosystem. It's all connected an so should be different scientific disciplines.
Stay tuned!
#resistancebreeding #soilmicrobiome #potato #phyotpathology #interdisciplinarity
#RegenerativeAgriculture highlighted as a transformative approach to ecological farming and soil recovery
August 21, 2025
Excerpt: "Ecological and societal co-benefits
"Indeed, the review outlines a range of co-benefits associated with regenerative agriculture, including enhanced carbon sequestration and potential #ClimateChange mitigation; reduced reliance on synthetic inputs, lowering emissions and pollution; #biodiversity restoration, both above and below ground; improved resilience to #drought, disease, and economic volatility; and possible public health benefits via improved crop quality and #SoilMicrobiome exposure.
The review notes growing scientific interest in links between soil health, crop nutrient density, and human health outcomes—highlighting RA's potential to contribute to broader public goals."
Read more:
https://phys.org/news/2025-08-regenerative-agriculture-highlighted-approach-ecological.html
A new critical review, published in the journal CABI Agriculture and Bioscience, highlights the emergence and scientific basis of regenerative agriculture—proposing a working definition centered on ecological cycles and farm system outcomes.
New paper out! Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome | Nature Biotechnology
https://www.nature.com/articles/s41587-025-02810-w
#soilmicrobiome #antibiotics #Bioinformatics #nanopore #ont #OpenAccess #naturebiotechnology #naturebiotech
Grâce à l’IA, elle identifie les bactéries clés qui soutiennent les fonctions essentielles du sol pour renforcer naturellement leur fertilité et leur résilience pour une agriculture durable.
📎 Plus d'infos: www.starfishbio.com
📩 [email protected]
#SoilMicrobiome #SoilHealth #Biosolutions
Wonderful mixture of techniques in this UK garden.
https://youtube.com/watch?v=2UVwfqPa4fg
5:55 has an explanation of syntropic farming. The theory is when densely planted support trees are pruned near the food tree; they send signals into the soil alerting to the damage, and this signal to put on fast above ground growth is picked by the food tree, which then grows quickly.
Does anyone know if there is evidence for this plant signaling and behaviour?
#permaculture
#Syntropic
#biology
#soilmicrobiome
Annals of Botany
Pierre Hohmann 🇺🇦
Biodiversa+
Benedikt Haug
DoomsdaysCW
Yozen Hernandez
NIOO-KNAW
JOBIM2025
robloblaw