TbasCO: Trait-based Comparative 'Omics Identifies Ecosystem-Level and Niche-Differentiating Adaptations of an Engineered Microbiome

Abstract

A grand challenge in microbial ecology is disentangling the traits of individual populations within complex communities. Various cultivation-independent approaches have been used to infer traits based on the presence of marker genes. However, marker genes are not linked to traits with complete fidelity, nor do they capture important attributes, such as the timing of expression or coordination among traits. To address this, we present an approach for assessing the trait landscape of microbial communities by statistically defining a trait attribute as shared transcriptional pattern across multiple organisms. Leveraging the KEGG pathway database as a trait library and the Enhanced Biological Phosphorus Removal (EBPR) model microbial ecosystem, we demonstrate that a majority (65%) of traits present in 10 or more genomes have niche-differentiating expression attributes. For example, while 14 genomes containing the high-affinity phosphorus transporter pstABCS display a canonical attribute (e.g. up-regulation under phosphorus starvation), we identified another attribute shared by 11 genomes where transcription was highest under high phosphorus conditions. Taken together, we provide a novel framework for revealing hidden metabolic versatility when investigating genomic data alone by assigning trait-attributes through genome-resolved time-series metatranscriptomics.