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

Abstract

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.

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

“…It is expected to reflect the range of different resources that can be transported or metabolized, together with flexibility in responses to different circumstances. Consistent with this interpretation, genome size is correlated with the proportion of the genome occupied with receiving internal and external signals and using those to modify gene expression, and also with aerobic metabolism and with sporulation (Nielsen et al, 2021).…”

“…This is a contributor to maximum growth rate and is quite widely used as a proxy for it (Nemergut et al, 2016;Niederdorfer et al, 2017;Valdivia-Anistro et al, 2016). However, reported correlations between RRN and maximum growth correspond to only moderate r 2 values in the range .15-.35 (Nielsen et al, 2021;Vieira-Silva & Rocha, 2010). Both maximum growth rate and RRN are expected to be most strongly under selection in lifestyles where resources become episodically available and there is a race to convert them into population.…”

“…Genome size is quite tightly characterized relative to the differences across species. For species with 10 or more records, median coefficient of variation was 3% (Nielsen et al, 2021). For maximum growth rate, fewer species are covered, the numbers are known less precisely, and variation across strains within species is hardly ever known.…”

“…Major habitat groups are considered as a potential influence. Relationships to aerobic versus anaerobic metabolism are discussed elsewhere (Nielsen et al, 2021).…”

Trait dimensions in bacteria and archaea compared to vascular plants

“…Genome size is known to vary across habitats, tending to be large in soils, small in thermal, gut, oral and intracellular species and intermediate in marine and fresh waters and sediments (Cobo‐Simón & Tamames, 2017; Nielsen et al 2021). This is consistent with an interpretation that soils present varied opportunities and challenges over time.…”