TbasCO: trait-based comparative ‘omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome

ISME Communications, vol. 2, pp. 111

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 gene 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 a 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 many genomes containing high-affinity phosphorus transporter pstABCS display a canonical attribute (e.g. up-regulation under phosphorus starvation), we identified another attribute shared by many genomes where transcription was highest under high phosphorus conditions. Taken together, we provide a novel framework for unravelling the functional dynamics of uncultivated microorganisms by assigning trait-attributes through genome-resolved time-series metatranscriptomics.

Authors 7

1. Elizabeth McDaniel corresponding

   University of Wisconsin–Madison

   Affiliation as printed

   Department of Bacteriology, University of Wisconsin—Madison , Madison, WI, USA

   Microbiology Doctoral Training Program, University of Wisconsin—Madison , Madison, WI, USA

2. Joris J.M. van Steenbrugge corresponding

   Netherlands Institute of Ecology · Wageningen University & Research

   Affiliation as printed

   Bioinformatics Group, Wageningen University and Research , Wageningen, The Netherlands

   Laboratory of Nematology, Wageningen University , Wageningen, The Netherlands

   Microbial Ecology, Netherlands Institute of Ecological Research , Wageningen, The Netherlands

3. Daniel R. Noguera

   University of Wisconsin–Madison

   Affiliation as printed

   Department of Civil and Environmental Engineering, University of Wisconsin—Madison , Madison, WI, USA

4. Katherine D. McMahon

   University of Wisconsin–Madison

   Affiliation as printed

   Department of Bacteriology, University of Wisconsin—Madison , Madison, WI, USA

   Department of Civil and Environmental Engineering, University of Wisconsin—Madison , Madison, WI, USA

5. Jos M. Raaijmakers Aachen Institute of Biology, Leiden University

   Leiden University · Netherlands Institute of Ecology

   Affiliation as printed

   Institute of Biology, Leiden University , Leiden, Netherlands

   Microbial Ecology, Netherlands Institute of Ecological Research , Wageningen, The Netherlands

6. Marnix H. Medema Aachen Institute of Biology, Leiden University

   Leiden University · Wageningen University & Research

   Affiliation as printed

   Bioinformatics Group, Wageningen University and Research , Wageningen, The Netherlands

   Institute of Biology, Leiden University , Leiden, Netherlands

7. Ben O. Oyserman corresponding

   Netherlands Institute of Ecology · Wageningen University & Research

   Affiliation as printed

   Bioinformatics Group, Wageningen University and Research , Wageningen, The Netherlands

   Microbial Ecology, Netherlands Institute of Ecological Research , Wageningen, The Netherlands

   Microbial Ecology, Netherlands Institute of Ecological Research, Wageningen, The Netherlands