Functional trait relationships demonstrate life strategies in terrestrial prokaryotes

• Published in: FEMS microbiology ecology Vol. 97; no. 5
• Main Authors: Finn, Damien R, Bergk-Pinto, Benoît, Hazard, Christina, Nicol, Graeme W, Tebbe, Christoph C, Vogel, Timothy M
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 19-05-2021; Wiley-Blackwell
• Subjects: Antimicrobial agents; Biodiversity and Ecology; Cluster analysis; Clustering; Differentiation; Ecology; Environmental Sciences; Environmental stress; Genomes; Glycosyltransferase; Microbiology; Niches; Oligotrophy; Oxidation resistance; Oxidative stress; Prokaryotes; Taxa; Taxonomy; Terrestrial environments; copiotroph-oligotroph; niche differentiation; Random Forest modelling; theoretical ecology
• ISSN: 1574-6941; 0168-6496; 1574-6941
• DOI: 10.1093/femsec/fiab068

ABSTRACT
Functional, physiological traits are the underlying drivers of niche differentiation. A common framework related to niches occupied by terrestrial prokaryotes is based on copiotrophy or oligotrophy, where resource investment is primarily in either rapid growth or stress tolerance, respectively. A quantitative trait-based approach sought relationships between taxa, traits and niche in terrestrial prokaryotes. With 175 taxa from 11 Phyla and 35 Families (n = 5 per Family), traits were considered as discrete counts of shared genome-encoded proteins. Trait composition strongly supported non-random functional distributions as preferential clustering of related taxa via unweighted pair-group method with arithmetic mean. Trait similarity between taxa increased as taxonomic rank decreased. A suite of Random Forest models identified traits significantly enriched or depleted in taxonomic groups. These traits conveyed functions related to rapid growth, nutrient acquisition and stress tolerance consistent with their presence in copiotroph-oligotroph niches. Hierarchical clustering of traits identified a clade of competitive, copiotrophic Families resilient to oxidative stress versus glycosyltransferase-enriched oligotrophic Families resistant to antimicrobials and environmental stress. However, the formation of five clades suggested a more nuanced view to describe niche differentiation in terrestrial systems is necessary. We suggest considering traits involved in both resource investment and acquisition when predicting niche.
Functional trait based modelling identified specific traits to explain certain Families that fill terrestrial copiotroph and oligotroph niches, but that overall microbial life strategies are more complex than this framework.