#FEMSmicroBlog: Physiology determines where an organism thrives


To thrive in an environmental niche and face its stress conditions, (micro)organisms need to have the right physiological capabilities. A new study ‘Functional trait relationships demonstrate life strategies in terrestrial prokaryotes’ published in FEMS Microbiology Ecology investigates how these physiological traits determine where an organism is able to survive. The first author of the study, Damien Finn, explains for the #FEMSmicroBlog how we can understand an organism’s preferred environmental niche based on their metabolic functionalities. #FascinatingMicrobes


Microbial metabolism optimized for the right niche

Organisms on this planet are perfectly adapted to the environmental niches they live in. As such, physiological capabilities – or traits – determine an organism’s ability to tackle the stress conditions it encounters in that particular environment.

These physiological traits can be shared among phylogenetically-related taxa at high (e.g. Phylum) and low (e.g. Family, Genus) taxonomic ranks. This implies that phylogeny, physiology and niche are closely linked.

The research article ‘Functional trait relationships demonstrate life strategies in terrestrial prokaryotes’ published in FEMS Microbiology Ecology assesses how organisms share physiological traits. Based on these results, the study aims to explain how different traits could determine the niche an organism occupies.

Physiological traits are closely linked to the phylogeny of an organism and determine its environmental niche.

The study focuses on 175 terrestrial prokaryote genomes, spanning 11 Phyla and 35 Families. The genomes originated from organisms that take part in various ecosystem processes including organic matter decomposition, nitrogen fixation, sinks or sources of greenhouse gases.

The traits shared between genomes are non-random. Hence, phylogeny is the most important factor in determining an organism’s traits. This further means that closely related taxa have more similar traits. However, the local environment, from which a taxon was isolated, partially affects this similarity.

For example, photosynthetic Cyanobacteria from geographically separated yet consistently nutrient-poor arid soils shared more traits with each other than methanogenic Euryarchaeota isolated from wetlands, rice paddies and waste ponds.

The study further showed that many functional traits are associated with particular Phyla and Families. These unique traits include metabolic capabilities like how organisms break down plant material, acquire nutrients, metabolise nitrogen, synthesise exopolysaccharides and whether cells preferentially respond to external environmental cues or changes in intracellular homeostasis.


Investing in growth or stress resistance

Depending on their metabolic preferences, microorganisms can be classified into copiotrophs and oligotrophs. Copiotrophs are organisms with relatively high growth rates, relatively poor growth efficiencies and high energy maintenance costs.

On the contrary, oligotrophs have low growth rates with high growth efficiencies but low energy maintenance requirements. Their metabolism allows them to better adapt to stress situations.

The copiotroph-oligotroph dichotomy model means to explain niche differentiation in microorganisms and separate traits into whether they facilitate rapid growth or provide stress tolerance mechanisms. However, according to this study, taxa do not split into these two groups.

Models to challenge the copiotrophic and oligotrohic lifestyles. Taxa split up into five clades rather than two.
Model for the five functional clades identified in Finn et al. (2021).

While several specific Proteobacteria Families met the assumptions for copiotrophs, and several diverse groups met those for oligotrophs, the majority of Families could not be considered as either. These ‘non-conformists’ might have evolved entirely distinct metabolic pathways (e.g. methane and ammonia metabolism, photosynthesis, fermentation) or unique physiological approaches (e.g. filamentous growth) to fill separate niches.


Challenging the copiotroph-oligotroph model

The concept of explaining niche differentiation as either copiotrophs or oligotrophs was adopted from macroecology. Based on this, plants and animals may differ in how they invest carbon and energy, yet are each fairly homogenous in how they acquire them.

In contrast, microorganisms have evolved a myriad of ways to extract carbon and energy from all sorts of sources that plants and animals cannot. In a space model representing niche separation, microbes can benefit from their additional traits to ‘spread out’ in space and further differentiate into their niches.

The previous copiotroph-oligotroph model solely considers traits linked to growth to predict the unique niche that a microbe fills in the environment. However, this study suggests taking traits into account that underlie both acquisition and investment of carbon and energy. Hence, this work highlights how these two metabolic functionalities work together and complement each other.

Read the article “Functional trait relationships demonstrate life strategies in terrestrial prokaryotes” published in FEMS Microbiology Ecology by Finn et al. (2021).


About the author of this blogDamien Finn

Dr Damien Finn is a postdoctoral researcher at the Thünen Institut für Biodiversität, Braunschweig, Germany, where his research focuses on soil microbial ecology, plant-microbe interactions, physical and chemical processes in soils, and how they are all linked. Perhaps to his detriment, he also has an unhealthy interest in theoretical ecology.

About this blog section

The section #FascinatingMicrobes for the #FEMSmicroBlog explains the science behind a paper and highlights the significance and broader context of a recent finding. One of the main goals is to share the fascinating spectrum of microbes across all fields of microbiology.

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