FEMS Microbiology Ecology Article Award 2021

01-03-22 Joseph Shuttleworth

Damien Finn, Benoît Bergk-Pinto, Christina Hazard, Graeme Nicol, Christoph Tebbe and Timothy Vogel are the winners of the best article award from FEMS Microbiology Ecology. The Editor-in-Chief and Senior Editors picked as their winning research article: Functional trait relationships demonstrate life strategies in terrestrial prokaryotes. We thank the authors for writing this excellent research paper. 

We interviewed all of the authors to find out more about the inspiration behind their paper:

Could you provide a brief, simple overview of the topic your paper covers?

Our Research article sought to identify the functions that distinguish 175 prokaryote species representative of different taxonomic groups frequently found in terrestrial ecosystems. We hypothesized that these taxonomic groups have evolved distinct repertoires of functions, or ‘life strategies’, that enable them to exploit different niches in terrestrial systems. Such niche differentiation is necessary for explaining how Proteobacteria, Actinobacteria etc. all coexist within a soil community. Apart from their ecological significance, these traits (functional profiles) can also be used to infer the specific roles of different taxonomic groups in important environmental processes, such as carbon and nitrogen cycling.

Furthermore, we were particularly interested in evaluating how well the framework of describing species as either ‘copiotrophs’ or ‘oligotrophs’ was supported by functional traits that distinguished taxonomic groups. Briefly, a copiotroph can be considered as an organism that invests its carbon and energy in rapid growth, whereas an oligotroph invests principally in biotic and environmental stress tolerance.

We identified a great variety of functional traits that differed between major phyla and families of terrestrial prokaryotes. By investigating these particular traits in greater detail, we could begin to separate taxa based on their ecological life strategies. For example, several specific proteobacterial Families (e.g. Pseudomonadaceae, Rhizobiaceae) agreed with the classical description of copiotrophs, and some diverse groups (e.g. Planctomycetales, Verrucomicrobia) as oligotrophs. However, most taxa possessed functional trait repertoires that fell outside this classical framework (e.g. Actinobacteria, Archaea), indicating its shortcomings in explaining prokaryote ecological life strategies. In addition, the acquisition of functions through gene transfer can add noise to the overall trend.”

Why is a more nuanced view to describe niche differentiation in terrestrial systems necessary?

We could observe that, while traits for rapid growth (e.g. ATP production, dealing with oxidative stress) and stress tolerance (e.g. sphingolipid production and antimicrobial resistance) are indeed important, they alone do not explain how taxa have differentiated to possess distinct life strategies. Our observations suggest an equally important role in how carbon and energy is acquired, in addition to how it is invested. For example, while proteobacterial Pseudomonadaceae and Nitrosomonadaceae share common traits for rapid growth, the former is better suited for competitively taking up nutrients via ABC and phosphotransferase transporters, whereas the latter performs autotrophic ammonia oxidation. By considering how a species both acquires and invests its carbon and energy, we could more meaningfully describe different ecological life strategies. For those interested in linking microbial ecology with terrestrial ecosystem processes, it may prove helpful to consider how any particular taxonomic group does both in tandem.”

What encouraged you to perform research in this area of microbiology?

Microbial ecologists, like us, study the diversity of environmental prokaryotic communities often by analyzing their 16S rRNA genes. However, a mere collection of such sequences is not much more than an inventory and does not provide a robust indication of ecological functions or potential interaction between organisms. This work was partially motivated by a need to prove (or disprove) what functions and characteristics are associated with taxonomy. Beyond this need, we were also driven by a theoretical question. The concept of niche differentiation is foundational to explaining the ecology of the organisms around us and how they have arrived at this point over evolutionary timescales. Naturally, we focused all these questions on prokaryotes, because they are the coolest living organisms on the planet.”

What do you see as the next steps in this area of research?

The concepts explored in this work can be improved upon in several ways. Firstly, a detailed study that compares more closely related species or even strains could provide a finer understanding of the specific traits that drive niche differentiation in soils and other habitats. Secondly, a severe limitation was that a function could not be assigned to 40 – 60% of the traits in each of our species. Indeed, this is a greater problem facing many recent studies of metagenome assembled genomes (MAGs) from environmental sources. It also highlights a continued need for culture-dependent and protein characterization work in microbial ecology. The more we understand the language of genomes, the better it is for identifying their genetic potentials, their emerging properties and their value for how life functions on this planet.”

Read the 2021 award winning paper: Functional trait relationships demonstrate life strategies in terrestrial prokaryotes

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