Cell size, genome size, and maximum growth rate are near‐independent dimensions of ecological variation across bacteria and archaea

Westoby, Mark; Nielsen, Daniel A.; Gillings, Michael R.; Litchman, Elena; Madin, Joshua S.; Paulsen, Ian T.; Tetu, Sasha G.

doi:10.1002/ece3.7290

Cited by 52 publications

(49 citation statements)

References 66 publications

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“…The roughly orthogonal position of several resistance and resilience traits in prokaryotes across whole range genome sizes reflects the results of some previous studies, which suggested that genome size and growth rate are not related (Vieira-Silva and Rocha, 2010; Westoby et al, 2021b).…”

Section: Synthesissupporting

confidence: 82%

“…We argue that nonmonotone relationships are the reason for contradicting findings e.g. the relationship between genome size and growth rates, that have been described as either positively related (Freilich et al, 2009;DeLong et al, 2010) or as largely unrelated dimensions (Vieira-Silva and Rocha, 2010; Westoby et al, 2021b). Furthermore, the previously reported superlinear positive correlation between genome size and HGT events (Cordero and Hogeweg, 2009b) or the assignment of generalist species to high %HGT, large CUBs or increased growth rates (Figure 2), which was not supported by our findings, could be due to the specific set of genomes that were used in the respective analyses.…”

Section: Synthesismentioning

confidence: 79%

“…A resistance-resilience tradeoff would instead imply a negative correlation between resistance associated traits, such as genome size or transcription factors versus resilience associated traits, such as rRNA gene copy numbers or growth rates. We want to point out that some studies did not find significant positive relationships between genome size and growth rates and although the observed correlation coefficients were positive, they were very weak (Vieira-Silva and Rocha, 2010; Westoby et al, 2021b). Still, also in these cases no negative correlations were detected as one would expect from a tradeoff between resistance and resilience.…”

Section: Trait-trait Correlations In the Light Of Physiological Constraintsmentioning

confidence: 92%

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Trait-trait relationships and tradeoffs vary with genome size in prokaryotes

Beier

Werner

Bouvier

et al. 2021

Preprint

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We report genomic traits that have been associated with the life history of prokaryotes and highlight conflicting findings concerning earlier observed trait correlations and tradeoffs. In order to address possible explanations for these contradictions we examined trait-trait variations of 11 genomic traits from ~ 17,000 sequenced genomes. The studied trait-trait variations suggested: (i) the predominance of two resistance and resilience-related orthogonal axes , (ii) an overlap between a resilience axis and an axis of resource usage efficiency. These findings imply that resistance associated traits of prokaryotes are globally decoupled from resilience and resource use efficiencies associated traits. However, further inspection of pairwise scatterplots showed that resistance and resilience traits tended to be positively related for genomes up to roughly five million base pairs and negatively for larger genomes. This in turn precludes a globally consistent assignment of prokaryote genomic traits to the competitor - stress-tolerator -ruderal (CSR) schema that sorts species depending on their location along disturbance and productivity gradients into three ecological strategies and may serve as an explanation for conflicting findings from earlier studies. All reviewed genomic traits featured significant phylogenetic signals and we propose that our trait table can be applied to extrapolate genomic traits from taxonomic marker genes. This will enable to empirically evaluate the assembly of these genomic traits in prokaryotic communities from different habitats and under different productivity and disturbance scenarios as predicted via the resistance-resilience framework formulated here.

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Section: Synthesissupporting

confidence: 82%

Section: Synthesismentioning

confidence: 79%

Section: Trait-trait Correlations In the Light Of Physiological Constraintsmentioning

confidence: 92%

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Trait-trait relationships and tradeoffs vary with genome size in prokaryotes

Beier

Werner

Bouvier

et al. 2021

Preprint

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“…Understanding general processes controlling the structure and function of microbiomes is a holy grail in microbial ecology. A functional trait-based perspective offers potential to elucidate microbial impacts on ecosystems through space and time to reveal such generalities ( 1 – 4 ). However, a challenge that microbial ecologists face is that trait-based classifications of microorganisms are historically conceptualized from theory generated for plants and animals.…”

Section: A Functional Trait-based Perspective For Microbial Ecologymentioning

confidence: 99%

Exploring Microbiome Functional Dynamics through Space and Time with Trait-Based Theory

et al. 2021

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“…Prokaryote genomes consist mainly (mean 88%) of protein‐coding genes, with much of the remainder devoted to structural RNAs or to regulation, and little non‐coding or parasitic DNA (Kirchberger et al 2020). Most genes are present as single copies, such that the count of different genes is closely correlated with genome size (r 2 = 0.976 across 3300 species in the Madin et al compilation, Westoby et al 2021). Prokaryote genomes are thought to be reduced in this way because of deletional bias (Mira et al 2001), deletion mutations being more common than insertions or duplications and leading to loss of genes or function.…”

Section: Introductionmentioning

confidence: 99%

Aerobic bacteria and archaea tend to have larger and more versatile genomes

Nielsen

Fierer

Geoghegan

et al. 2021

Oikos

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How well can ecological strategies of bacteria and archaea be characterized via quantitative traits? Bacteria with larger genome size are more versatile. They can transport and metabolise a wider range of substrates. More of their genome is engaged in signal detection and response, indicating they benefit from different resources at different times or under different conditions. Across cultured species aerobes were shown to average ca 35% larger genomes than anaerobes, after accounting for the previously-known decline in genome size with temperature. Aerobic habitats might well present opportunities and challenges that vary through time more than anaerobic habitats. Synthesis A recent compilation of traits across culturable species of bacteria and archaea allows relationships to be quantified between genome size and other traits and habitat. Cell morphology, size, motility, sporulation and doubling time were not strongly correlated with genome size. Aerobic species averaged ca 35% larger genomes than anaerobic, adjusted for growth temperature. Aerobes had a similar mix of gene functions compared to anaerobes of the same genome size. Shifting proportions of aerobes to anaerobes accounted for about half of previously-known differences in mean genome size between habitats. One possible factor in these results could be if effective population sizes are larger for aerobes, reducing the potential for gene loss via genetic drift. Larger genomes also confer versatility. They can transport and metabolise a wider range of substrates. More of their genome is engaged in signal detection and response, indicating they benefit from different resources at different times or under different condition. Aerobic habitats might well present opportunities and challenges that vary through time more than anaerobic habitats. The genome size trait-dimension contributes a useful quantitative descriptor for ecological strategies.

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Cell size, genome size, and maximum growth rate are near‐independent dimensions of ecological variation across bacteria and archaea

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 52 publications

References 66 publications

Trait-trait relationships and tradeoffs vary with genome size in prokaryotes

Trait-trait relationships and tradeoffs vary with genome size in prokaryotes

Exploring Microbiome Functional Dynamics through Space and Time with Trait-Based Theory

Aerobic bacteria and archaea tend to have larger and more versatile genomes

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