Microbial species: some papers

One of the things I have previously discussed (see the “Best of ET” tab) is microbial species concepts. Two new papers have come out on this, and it seems to be a hot research topic right now.

Eppley, et al., in the journal Genetics, argue that the claim that I happened to make in my as-yet unpublished paper in History and Philosophy of the Life Sciences, that microbial species are clusters of genomes maintained by, among other things, homologous recombination of genes, is supported by experimental evidence based on genomic data of two microbial species of Archae bacteria, of the genus Ferroplasma. They sequenced the genomes and compared the homology and exchange of genes over the entire sequence, and compared the evidence for recombination based on sequence identity.

FIGURE 2.— Images showing the clear separation of the Ferroplasma type I (brown) and Ferroplasma type II (blue) genomes. (A) Reads from the community genomic data set are aligned (using BLASTN) to 2.7 kb of the isolate genome of F. acidarmanus and displayed as described in Figure 1. Reads are grouped (indicated by background shades of blue and brown) on the basis of conserved SNP patterns. Genes encoded on this fragment (bars on top from left to right) are a hypothetical protein, a putative dihydroxy-acid dehydratase, and a putative acetolactate synthase (large subunit). (B) The genomewide distribution of read sequence alignments against the F. acidarmanus genome. Every 3000 bases, all overlapping reads were assigned to one or the other Ferroplasma type and the divergence of each read from F. acidarmanus was calculated. At each point, for each type, the 5, 25, 33, 66, 75, and 95% divergence quantiles were calculated. These points were then connected to map the distributions of sequence identity genomewide. Lightly shaded regions span the 5–95% quantiles; darker regions, the 25–75% quantiles; and the darkest region, the 33–66% quantiles.

The above figure indicates the differences between the species of Ferroplasma bacteria in a microbial community taken from a mine in California. Their conclusion is that several lines of evidence indicate that recombination depends on the average sequence identity being high – much higher than the observed identity of the majority of genes in the two species.This, then, tends to maintain the clusters of these otherwise asexual organisms as distinct groups.

A second paper in PLoS Biology by de Visser reports the results of experiments on gene exchange as a form of sex, hedging against selective sweeps, in the asexual bacteria Escheria coli, the common gut bacterium. By inserting genes into various strains, Tim Cooper was able to test Weismann’s hypothesis that sex serves to increase the fitness of organisms by reducing competition between beneficial mutations. The Fisher-Muller hypothesis is that sex is advantageous because it allows beneficial mutations that arise in different lineages to recombine, thereby reducing clonal interference and speeding adaptation. The results not only validate the F-M hypothesis, but also indicate how plasmid-mediated gene exchange in bacteria might serve to do the same thing, and thus serve to isolate strains of otherwise asexual organisms into species.