Into the microbial niche

Lucie A Malard; Antoine Guisan

doi:10.1016/j.tree.2023.04.015

Into the microbial niche

Trends Ecol Evol. 2023 Oct;38(10):936-945. doi: 10.1016/j.tree.2023.04.015. Epub 2023 May 24.

Authors

Lucie A Malard¹, Antoine Guisan²

Affiliations

¹ Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland. Electronic address: lucie.malard@unil.ch.
² Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland; Institute of Earth Surface Dynamics, University of Lausanne, 1015 Lausanne, Switzerland.

PMID: 37236880
DOI: 10.1016/j.tree.2023.04.015

Abstract

The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.

Keywords: environmental niche; metabolic niche; metagenomics; metatranscriptomics; microbial communities.

Publication types

Review

MeSH terms

Ecosystem*
Metagenomics*