Modelling soil prokaryotic traits across environments with the trait sequence database ampliconTraits and the R package MicEnvMod

作者：Jonathan Donhauser, Anna Doménech‐Pascual, Xingguo Han, Karen Jordaan, Jean‐Baptiste Ramond, Aline Frossard, Anna M. Romaní, Anders Priemé · 发表于：Ecological Informatics · 年份：2024 · DOI：10.1016/j.ecoinf.2024.102817 · 被引用次数：11 · 研究领域：Microbial Community Ecology and Physiology、Genomics and Phylogenetic Studies、Soil Carbon and Nitrogen Dynamics

We present a comprehensive, customizable workflow for inferring prokaryotic phenotypic traits from marker gene sequences and modelling the relationships between these traits and environmental factors, thus overcoming the limited ecological interpretability of marker gene sequencing data. We created the trait sequence database ampliconTraits , constructed by cross-mapping species from a phenotypic trait database to the SILVA sequence database and formatted to enable seamless classification of environmental sequences using the SINAPS algorithm. The R package MicEnvMod enables modelling of trait – environment relationships, combining the strengths of different model types and integrating an approach to evaluate the models' predictive performance in a single framework. Traits could be accurately predicted even for sequences with low sequence identity (80 %) with the reference sequences, indicating that our approach is suitable to classify a wide range of environmental sequences. Validating our approach in a large trans-continental soil dataset, we showed that trait distributions were robust to classification settings such as the bootstrap cutoff for classification and the number of discrete intervals for continuous traits. Using functions from MicEnvMod, we revealed precipitation seasonality and land cover as the most important predictors of genome size. We found Pearson correlation coefficients between observed and predicted values up to 0.70 using repeated split sampling cross ...