What happens to bacterial communities under selection?

When one gene comes under a new selection pressure, a population can respond by increasing the frequency of the better alleles. This can involve directional selection, whereby the population shifts towards the new optimum, and/or it can entail stabilizing selection, where the genetic diversity of the population decreases. In both cases allele frequencies change, and this is what (biological) evolution is.

This is all fairly straightforward. However, when there are many populations that are distinct species, and they all come under the same new selection pressure, then what is that? If we can detect selection between these distinct populations, is that still evolution? It is not evolution in the traditional sense, which center its attention on what happen within a population. So if we’re not looking at what happens within one population, can we even say that we are studying evolution?

In a previous post I explained how we have used metagenomics to retrieve DNA sequences of a specific gene called nitrite reductase (nirK) that soil bacteria use to obtain energy from fertilizer. When sequencing the soil only a limited set of sequences are discovered. Imagine then that some species are more abundant in the soil than others. Because it is random with respect to which species they come from, we are then clearly more likely to retrieve sequences from the most abundant species. There are many bacterial species that has a copy of nirK, and we are limited in how many sequences we can obtain. Many species will therefore not be represented in our sample.

Now, comparing these sequences is done using the formalism of d_N/d_S, which measures the ratio between non-synonymous nucleotide substitutions and synonymous substitutions (substitutions that change an amino acid vs. those that do not). d_N/d_S (also designated by ω) is measured between species, so it is perfect for the sequences we have. The analysis showed that ω is very low, indicating purifying selection – there are more synonymous nucleotide changes compared to non-synonymous changes than expected if both were equally likely. That means that nirK is being constrained and optimized, presumably because the gene carries out an important function for the bacteria. Changes to the resulting protein are not tolerated, though a little variation in the amino acid sequence between the species does exist.

Furthermore, different environments were compared. In one environment, deciduous forest (DF), the soil is not fertilized. In another environment used for standard agriculture (AG), the soil is fertilized. The analysis showed that the sequences in AG are under stronger purifying selection than sequences in DF (figure 1). Presumably this is because the conditions in AG make it more favorable and more important to have a really good copy of nirK that can help the bacteria to obtain energy from the nitrate in the fertilizer.

Figure 1. dN/dS is smaller in Ag than in DF, indicating that there is stronger purifying selection in AG compare to DF. ES and SF are environments that have not been used for agriculture for about 20 and 40 years, respectively.

So far, so good. Now here is my question. Given that the bacteria experience purifying selection, do we really know what is happening to the community of species? Take a look at the following figure.

Figure 2. An artist’s representation of different populations in two-dimensional amino acid space. Click to enlarge.

The farther sequences are from each other, the fewer amino acids they have in common. In (A) several species of bacteria can be seen, each represented by a Gaussian distribution, where the darkest points are the more abundant sequences. The red cross represents the optimal sequence (need there be only one?), but because bacteria in DF get most of their energy from oxygen, nirK is of relatively little consequence. In (B) and (C), AG has been loaded with fertilizer, so now there is ample opportunity to get energy from that. Therefore the species experience a pull towards the optimal sequence. In (B) this results in each of the population shifting their distribution towards to optimum, while in (C) they do not shift, but instead the species that are already closer to the optimum experience an increases in carrying capacity, such that they become more abundant compared to species that are farther away from the optimum.

d_N/d_S basically measures this distance in amino acid space, and clearly this distance is on average diminished in (B). However, because we are more likely to retrieve sequences from the more abundant species, the average distance between sequences is also diminished in (C). In other words, both models are consistent with d_N/d_S being lower in AG, and we therefore cannot say what is really going on in the soil. Is there a way to distinguish between the two models? Could we take some bacteria to the lab and grow them under DF and AG like conditions, and then figure this out? Is there a third model that can explain the data as well?

And then the question of evolution – is this even evolution? Some biologists simply call this species sorting, and dismiss that it is evolution. However, I argue that it is evolution, because what we are observing is the effect of natural selection, which in (B) causes a change in allele frequencies within each population, and in (C) because it changes abundance that can lead to long-term changes in community structure.

Evolution or not? What do you think? Cross-posted on BEACON's blog.