Bacteria and Archaea absorb available nutrients quickly, and both rapid deployment of metabolic proteins and rapid reproduction are key to the exploitation of patchily distributed nutrients. As the majority of a prokaryote’s DNA is arrayed in a single circular chromosome, speed of replication allows for speed of reproduction. As a result, selection favors those strains of Bacteria and Archaea that retain only the genetic material vital to the organism.
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Eukaryotes have multiple linear chromosomes and can begin replication from many sites on each one. Eukaryotes are thus able to replicate multiple strands of DNA simultaneously and rapidly (Chapter 12). This ability relieves the evolutionary pressure for streamlining, allowing eukaryotic genomes to build up large amounts of DNA that do not code for proteins. Most of this additional DNA was originally considered to have no function and, indeed, was called “junk DNA.” That view, however, has been modified in recent years, as the complete genome has come to be better understood (Chapter 13). Eukaryotic genomes appear to contain truly junky DNA, but at least some of the DNA that does not code for proteins functions in gene regulation (Chapter 19). This regulatory DNA gives eukaryotes the fine control of gene expression required for both multicellular development and complex life cycles, two major features of eukaryotic diversity.
At this point, it can be seen that the evolutionary success of eukaryotes rests on a combination of features. The innovations of dynamic cytoskeletal and membrane systems gave eukaryotes the structure required for larger cells with complex shapes and the ability to ingest other cells. Thus, early unicellular eukaryotes did not gain a foothold in microbial ecosystems by outcompeting bacteria and archaeons. Instead, they succeeded by evolving novel functions. Along with the capacity to remodel cell shape, eukaryotes evolved complex patterns of gene regulation, which in turn enabled unicellular eukaryotes to evolve complex life cycles and multicellular eukaryotes to generate multiple, interacting cell types during growth and development. These abilities opened up still more possibilities for novel functions, which we explore in this and later chapters.
Quick Check 1 How did the evolutionary expansion of eukaryotic organisms change the way carbon is cycled through biological communities?
In general, eukaryotes employ a subset of the metabolic pathways used by bacteria. Most eukaryotes are capable of aerobic respiration; most can also gain at least some energy by fermentation; and some can also photosynthesize. In many ways, then, carbon cycling by eukaryotes is much like carbon cycling by aerobic prokaryotes. The novel contribution of eukaryotes is the ability to capture and ingest other cells, thus introducing predation into the carbon cycle.