Novel model-based clustering reveals ecologically differentiated bacterial genomes across a large climate gradient

Date

2019

Authors

Simonsen, Anna
Barrett, Luke G.
Thrall, Peter H.
Prober, Suzanne M.

Journal Title

Journal ISSN

Volume Title

Publisher

Blackwell Publishing Ltd

Abstract

A pervasive challenge in microbial ecology is understanding the genetic level where ecological units can be differentiated. Ecological differentiation often occurs at fine genomic levels, yet it is unclear how to utilise ecological information to define ecotypes given the breadth of environmental variation among microbial taxa. Here, we present an analytical framework that infers clusters along genome‐based microbial phylogenies according to shared environmental responses. The advantage of our approach is the ability to identify genomic clusters that best fit complex environmental information whilst characterising cluster niches through model predictions. We apply our method to determine climate‐associated ecotypes in populations of nitrogen‐fixing symbionts using whole genomes, explicitly sampled to detect climate differentiation across a heterogeneous landscape. Although soil and plant host characteristics strongly influence distribution patterns of inferred ecotypes, our flexible statistical method enabled us to identify climate‐associated genomic clusters using environmental data, providing solid support for ecological specialisation in soil symbionts.

Description

Keywords

Bacteria, ecological differentiation, ecotype, soil, symbiont

Citation

Source

Ecology Letters

Type

Journal article

Book Title

Entity type

Access Statement

License Rights

Restricted until

2099-12-31