So yes I am trying to catch up with my Microbial advent Calendar and No, I am not redoing the same as day 06 of the Microbial Advent Calendar… NO WAIT!! COME BACK!! I swear, it different and it’s linked in a nice way! (At least I think it is…)
Today’s paper (here) was suggested by my esteemed, and former, colleague Niko Lesich (Twitter). The study, from Kleinteisch and 14 other collaborators, looked at one sexy question in microbial ecology, the biogeography of microorganisms, this time on a pole to pole scale. Indeed, they sampled terrestrial and lacustrine biofilms from Arctic, Antarctic and temperate regions. Using amplicon libraries of a variable region of the 16S rRNA, they ought to have a look if the adage of microbiologist saying “Everything is everywhere” is right.
For macroecology the idea of biogeography is easy to understand, if you are a gazelle and you are stuck on an island, you dispersal on the planet might be limited. However, for microorganisms, physical barriers are less constraining and dispersal can happen on considerable larger distances. In this case, local as well as more cosmopolitan species are expected to be present and species distributions are likely to reflect environmental filtering rather than dispersal limitations.
The study looked at roughly a 100 samples from both poles, Europe and New Zealand*, and what they found is that samples from both poles have a larger fraction of overlapping OTU than there geographically closer temperate region. It proposes that, in addition to endemic taxa, there is a pool of cosmopolitan bacteria with widespread dispersal capacities, from which certain species and strains are selected for their capability to sustain themselves in polar environments.
Fine bacteria adapted to cold survive better in similar environments, they can travel long distances but always remain in very low abundance until they find the next whisky bar, adequate environment. But then what if we put this paper in parallel to the one from day 06 of the Microbial Advent Calendar (here), where we looked at two cousins from each pole. Similar but different. Very similar on the 16S rRNA level, as today study suggests, but then on a functional (gene content wise) level there were quite some differences, notably on the metabolic pathways distribution. Those metabolic differences were thought to be present because of some fine-scale environmental differences between the pole. I think that here there is another level of selection from the environment, where one overarching condition select the species with the capacity to adapt (here cold) but then still need to finely tune its genome to properly fit.
Even if I am quickly comparing at 22h in the evening only two genomes and some partial 16S rRNA data, these studies still show more or less the same concept: High bacteria dispersal, environmental selections and bacterial plasticity.
*: So I had this paper as a note and read it quickly on the plane to Switzerland. I thought it would be a nice story. However, rereading the paper while writing this blog post I found out that there is a large discrepancy in the sample size. There are 89 Arctic and Antarctic samples, 5 Europeans one and 7 from the southern island of New Zealand. Besides the fact that it is apparently easier to have sampled from the remote poles than local Europe, from the M&M section on the statistical analysis you can read:
“To determine the number of shared taxa between major regions, for each region the same number of samples with the largest number of reads were pooled. This pooled matrix was rarefied to the same depth for all regions and the overlap in OTUs shared between the regions calculated using the vennCounts function from the R-package limma.”
I am a little bit worried about this in fact. It seems that there nice oversampling analysing is in the end reduced to comparing 20 samples together… uuuuuuh….
Man… I do not have time to get into the details, I have another post to write tonight…