Streamlining theory

Genomic streamlining is a hypothesis in evolutionary biology and microbial ecology that suggests that there is a reproductive benefit to prokaryotes having a smaller genome size with less non-coding DNA and fewer non-essential genes. There is a lot of variation in prokaryotic genome size, with the smallest free-living cell’s genome being roughly ten times smaller than the largest prokaryote. Two of the bacterial taxa with the smallest genomes are Prochlorococcus and Pelagibacter ubique, both highly abundant marine bacteria commonly found in oligotrophic regions. Similar reduced genomes have been found in uncultured marine bacteria, suggesting that genomic streamlining is a common feature of bacterioplankton. This theory is typically used with reference to free-living organisms in oligotrophic environments.

Theory Overview

Comparison of genome sizes across select organisms

Genome streamlining theory states that certain prokaryotic genomes tend to be small in size in comparison to other prokaryotes, and all eukaryotes, due to selection against the retention of non-coding DNA. The known advantages of small genome size include faster genome replication for cell division, fewer nutrient requirements, and easier co-regulation of multiple related genes, because gene density typically increases with decreased genome size. This means that an organism with a smaller genome is likely to be more successful, or have higher fitness, than one hindered by excessive amounts of unnecessary DNA, leading to selection for smaller genome sizes.

Some mechanisms that are thought to underlie genome streamlining include deletion bias and purifying selection. Deletion bias is the phenomenon in bacterial genomes where the rate of DNA loss is naturally higher than the rate of DNA acquisition. This is a passive process that simply results from the difference in these two rates. Purifying selection is the process by which extraneous genes are selected against, making organisms lacking this genetic material more successful by effectively reducing their genome size. Genes and non-coding DNA segments that are less crucial for an organism survival will be more likely to be lost over time.

This selective pressure is stronger in large marine prokaryotic populations, because intra-species competition favours fast, efficient and inexpensive replication. This is because large population sizes increase competition among members of the same species, and thus increases selective pressure and causes the reduction in genome size to occur more readily among organisms of large population sizes, like bacteria. This may explain why genome streamlining seems to be particularly prevalent in prokaryotic organisms, as they tend to have larger population sizes than eukaryotes.

It has also been proposed that having a smaller genome can help minimize overall cell size, which increases a prokaryotes surface-area to volume ratio. A higher surface-area to volume ratio allows for more nutrient uptake proportional to their size, which allows them to outcompete other larger organisms for nutrients. This phenomenon has been noted particularly in nutrient deplete waters.