Compositionality, sparsity, spurious heterogeneity, and other data-driven challenges for machine learning algorithms within plant microbiome studies

S Busato, M Gordon, M Chaudhari, I Jensen… - Current opinion in plant …, 2023 - Elsevier
The plant-associated microbiome is a key component of plant systems, contributing to their
health, growth, and productivity. The application of machine learning (ML) in this field …

The power of forecasts to advance ecological theory

ASL Lewis, CR Rollinson, AJ Allyn… - Methods in Ecology …, 2023 - Wiley Online Library
Ecological forecasting provides a powerful set of methods for predicting short‐and long‐term
change in living systems. Forecasts are now widely produced, enabling proactive …

The temperate forest phyllosphere and rhizosphere microbiome: a case study of sugar maple

M Enea, J Beauregard, T De Bellis, M Faticov… - Frontiers in …, 2025 - frontiersin.org
The interactions between sugar maple (Acer saccharum, Marshall) and its microbial
communities are important for tree fitness, growth, and establishment. Despite recent …

Depth effects on bacterial community altitudinal patterns and assembly processes in the warm-temperate montane forests of China

L He, X Sun, S Li, W Zhou, J Yu, G Zhao, Z Chen… - Science of The Total …, 2024 - Elsevier
Soil bacterial communities are essential for ecosystem function, yet their response along
altitudinal gradients in different soil strata remains unclear. Understanding bacterial …

[HTML][HTML] Soil function-microbial diversity relationship is impacted by plant functional groups under climate change

RH Jayaramaiah, CSC Martins, E Egidi… - Soil Biology and …, 2025 - Elsevier
Understanding the interactions between plant and soil microbial diversity is crucial for
predicting ecosystem responses to environmental changes. While the individual roles of …

Predicting microbial community compositions in wastewater treatment plants using artificial neural networks

X Liu, Y Nie, XL Wu - Microbiome, 2023 - Springer
Background Activated sludge (AS) of wastewater treatment plants (WWTPs) is one of the
world's largest artificial microbial ecosystems and the microbial community of the AS system …

Habitat partitioning of soil microbial communities along an elevation gradient: from plant root to landscape scale

L Merino‐Martín, D Hernández‐Cáceres, F Reverchon… - Oikos, 2023 - Wiley Online Library
Within a landscape, multiple habitats exist for soil microbial communities. But how these
habitats shape community composition requires an understanding of the way in which …

Forest structural diversity is linked to soil microbial diversity

AK Lang, EA LaRue, SN Kivlin, JD Edwards… - …, 2023 - Wiley Online Library
Efforts to catalog global biodiversity have often focused on aboveground taxonomic
diversity, with limited consideration of belowground communities. However, diversity …

Forest thinning alleviates the negative effects of precipitation reduction on soil microbial diversity and multifunctionality

H Wang, D Chen, C Wu, L Guo, X Sun… - Biology and Fertility of …, 2023 - Springer
Thinning is an important forest management practice to mitigate the adverse effects of
increased drought on tree growth and productivity. However, the responses of the soil …

Understory vegetation diversity, soil properties and microbial community response to different thinning intensities in Cryptomeria japonica var. sinensis plantations

KL Liu, BY Chen, B Zhang, RH Wang… - Frontiers in …, 2023 - frontiersin.org
Introduction Soil microorganisms are the key factors in elucidating the effects of thinning on
tree growth performance, but the effects of vegetation and soil on the species composition …