Evolution of a minimal cell

Lennon, Jay T.; Moger-Reischer, Roy Z.; Glass, John I.; Wise, Kim S.; Bittencourt, Daniela; Sun, Lijie; Lynch, Michael

doi:10.1101/2021.06.30.450565

Cited by 5 publications

(6 citation statements)

References 69 publications

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“…S12, S14). This finding supports previous reports of microbes that are abundant in deep subsurface environments including the sulfate-reducing Candidatus Desulforudis audaxviator (65-67), Spirochaeta (68) or organisms affiliating with (Cald)atribacteriota (69)(70)(71)(72)(73)(74)(75). In contrast, Cyanobacteria, Bdellovibrionota, Fusobacteriota, Verrucomicrobiota, Planctomycetota, Bacteroidota, Campilobacterota, and Proteobacteria are more widespread in surface ecosystems.…”

Section: Abundant Microbial Lineages In the Subsurfacesupporting

confidence: 91%

A global atlas of subsurface microbiomes reveals phylogenetic novelty, large scale biodiversity gradients, and a marine-terrestrial divide

Ruff,

Hrabe de Angelis,

Mullis

et al. 2024

Preprint

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Subsurface environments constitute one of Earth's largest habitats for microbial life, yet differences between surface and subsurface microbiomes and between marine and terrestrial microbiomes remain unclear. We analyzed 478 archaeal and 1054 bacterial amplicon sequence datasets and 147 metagenomes from diverse and globally distributed surface and subsurface environments. Taxonomic analyses show that archaeal and bacterial diversity is similar in marine and terrestrial microbiomes at local to global scales. However, community composition greatly differs between marine and terrestrial microbiomes, suggesting a horizontal phylogenetic divide between sea and land that mirrors patterns in plant and animal diversity. In contrast, community composition overlapped from surface to subsurface environments indicating vertical diversity continua rather than a discrete subsurface biosphere. Diversity of terrestrial microbiomes decreases from surface to subsurface environments. Marine subsurface diversity and phylogenetic novelty rivaled (bacteria) or even exceeded (archaea) that of surface environments, suggesting that the marine subsurface holds a considerable and underestimated fraction of Earth's archaeal and bacterial diversity.

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Section: Abundant Microbial Lineages In the Subsurfacesupporting

confidence: 91%

A global atlas of subsurface microbiomes reveals phylogenetic novelty, large scale biodiversity gradients, and a marine-terrestrial divide

Ruff,

Hrabe de Angelis,

Mullis

et al. 2024

Preprint

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“…Smaller bacteria, with higher surface area:volume ratios and hence the potential for higher membrane-bioenergetic capacity, have reduced growth rates owing to the increased relative investment in the cell membrane itself 50 . Notably, strong selection for increased growth rate can yield a successful response in lab cultures of bacteria, but this seems always to be accompanied by an increase in cell volume and/or decrease in surface area:volume ratio [87][88][89] . All of these observations are quite contrary to the hypothesis that constraints on the upper limit to bacterial cell size imposed by membrane-bioenergetic limitations were solved by the evolution of mitochondria 30 .…”

Section: Discussionmentioning

confidence: 99%

Evolutionary scaling of maximum growth rate with organism size

Lynch

Trickovic

Kempes

2022

Sci Rep

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Data from nearly 1000 species reveal the upper bound to rates of biomass production achievable by natural selection across the Tree of Life. For heterotrophs, maximum growth rates scale positively with organism size in bacteria but negatively in eukaryotes, whereas for phototrophs, the scaling is negligible for cyanobacteria and weakly negative for eukaryotes. These results have significant implications for understanding the bioenergetic consequences of the transition from prokaryotes to eukaryotes, and of the expansion of some groups of the latter into multicellularity. The magnitudes of the scaling coefficients for eukaryotes are significantly lower than expected under any proposed physical-constraint model. Supported by genomic, bioenergetic, and population-genetic data and theory, an alternative hypothesis for the observed negative scaling in eukaryotes postulates that growth-diminishing mutations with small effects passively accumulate with increasing organism size as a consequence of associated increases in the power of random genetic drift. In contrast, conditional on the structural and functional features of ribosomes, natural selection has been able to promote bacteria with the fastest possible growth rates, implying minimal conflicts with both bioenergetic constraints and random genetic drift. If this extension of the drift-barrier hypothesis is correct, the interpretations of comparative studies of biological traits that have traditionally ignored differences in population-genetic environments will require revisiting.

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“…Cell volumes were converted to S/V using the empirical scaling S = 2 πV 2 / 3 reported to hold across many bacterial species [43]. Second, we collected relative fitness and cell size of wild-type Mycoplasma mycoides and M. mycoides whose genome has been minimized by removal of non-essential genes [44]. Comparing LTEE data with our analytical model (Fig 5), we find that the observed scaling falls very near to the expected scaling for E. coli grown in the media with similar composition (M63) as that used in LTEE (Davis broth with glucose).…”

Section: Resultsmentioning

confidence: 99%

Resource allocation to cell envelopes and the scaling of bacterial growth rate

Trickovic

Lynch

2022

Preprint

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Although various empirical studies have reported a positive correlation between the specific growth rate and cell size across bacteria, it is currently unclear what causes this relationship. We conjecture that such scaling occurs because smaller cells have a larger surface-to-volume ratio and thus have to allocate a greater fraction of the total resources to the production of the cell envelope, leaving fewer resources for other biosynthetic processes. To test this theory, we developed a coarse-grained model of bacterial physiology composed of the proteome that converts nutrients into biomass, with the cell envelope acting as a resource sink. Assuming resources are partitioned to maximize the growth rate, the model yields expected scalings. Namely, the growth rate and ribosomal mass fraction scale negatively, while the mass fraction of envelope-producing enzymes scales positively with surface-to-volume. These relationships are compatible with growth measurements and quantitative proteomics data reported in the literature.

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Evolution of a minimal cell

Cited by 5 publications

References 69 publications

A global atlas of subsurface microbiomes reveals phylogenetic novelty, large scale biodiversity gradients, and a marine-terrestrial divide

A global atlas of subsurface microbiomes reveals phylogenetic novelty, large scale biodiversity gradients, and a marine-terrestrial divide

Evolutionary scaling of maximum growth rate with organism size

Resource allocation to cell envelopes and the scaling of bacterial growth rate

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