Caporaso et al. were
specifically interested in the seasonal species diversity and richness changes
at one sampling location in the Western English Channel. Previous studies have
reported strong seasonal patterns in community dynamics at this location and
the paper itself wanted to understand what was driving the patterns. They went
about this by testing two opposing hypothesises; either the observed changes
were driven by absolute changes in community composition (as the previous
studies would suggest), or, that the changes were driven by differences in
relative abundance of the same community members.
The paper used an entirely genomic method. They compared one
very detailed sequenced sample (called the deep sequence) to many less detailed
samples taken every month from January 2003 – December 2008 (called shallow
sequences); the specific genome zone they looked at was V6 hypervariable region
of our good friend the 16S rRNA gene. They found that when all the shallow
samples were added together over the six year period, 95.47% of the operational
taxonomic units were present in the single deep sequence. Furthermore when each
shallow sample was compared individually with the single deep sample, an
average of 99.75% operational taxonomic units present, were the same. They also
used rarefaction (a statistical method to predict the maximum number of species
actually present) and, despite analysing over 10 million 16s rRNA fragments,
they did not reach the assumptotal predicted by rarefaction. This indicates
that there is still some incredible rare species not yet discovered in this
ecosystem.
Importantly this study provides evidence that traditionally
observed seasonal changes diversity are actually driven by the relative
abundance of the same taxonomic groups, rather than absolute changes in
community as was previously thought.
Essentially this was revealed by very in depth sequencing which
accounted for small branch length changes between classifiable and
unclassifiable taxonomic units which traditional methods cannot detect. The
findings suggest that the ecosystem at the sampled site has a huge core
microbiome, which potentially changes the way we think about selection
pressures and evolution. Is selection acting on the level of an individual
microbe? Or is selection acting on the whole microbiome? Inside which we know
genes are easily transferable via horizontal gene transfer. This study doesn’t
provide any evidence for or against this, but I just thought I’d
highlight it as a possibility…
Caporaso,
J. G., Paszkiewicz, K., Field, D., Knight, R., & Gilbert, J. A. (2012). The Western English Channel contains a
persistent microbial seed bank. The ISME journal, 6(6), 1089–93.
Hi Vicky
ReplyDeletejust making sure that I have understood this: they are saying that OTU richness (total number of OTU) remains the same and that only the relative abundance changes? Did they propose how this change in abundance should be quantified in future? Because as you pointed out, there is often confusion in the literature as to measuring microbial community changes. For instance, Thiele et al. (2012)(the rather interesting ocean fertilization paper..) applied Shannon and Simpson indexes using genus (at least not species), without mentioning assumptions and limitations.
You mention the possible influence in horizontal gene transfer and how selection potentially acts on different levels, could you develop your ideas a bit further? Selection should favour organisms with the optimal genome for surrounding environment, similarly acquiring genes to cope with a variety of environments should be an advantage and selected for. But in reality what we find is a diversity of genomes and not a single perfectly adapted organism. Would be interesting to discuss in relation to symmorphosis..
Hi Anna,
DeleteYes that’s right, the same members were present throughout but the relative abundance of each changed, and importantly they were only able to discover this by using a super in-depth sequencing system called an “Illumina GAIIx” which provided approximately a one thousand fold deeper coverage. In terms of future study, the authors recommend that more researchers use this superior in-depth sequencing protocol. As for the diversity measures they were mainly interested in the total OTU by they also measured community dissimilarity, measured by unweighted UniFrac, which is a kind of multivariate analysis which provides a map with lots of dots on which you can then visually interpret patterns from.
Moving onto my selection pressure comment I would love to explore this idea further, the reason I didn’t do so in the post is because I didn’t want to take away from what this study really found which was based on diversity and community composition. My inferences from these finding lead me to think about evolution as a process. In the site sampled there was one huge core biome which was present throughout the six year period, whilst there was fluctuations of relative abundance there is little evidence for extinction or total dominance of any individual OTU. Evolutionary theory states that selection acts on the phenotype, or put another way the individual and the genotype that encodes it, however, as we progress through this microbiology module the lines are blurring significantly. What even is an individual when they are all constantly swapping genes as well as forming close association and symbioses with other organisms? This idea is linked to the one ocean model (O’dor et al., 2009) which I suggest you read about if you’re really interested about this. You make an interesting link to symmorphosis and optimality which I think might be related to the cost/benefit trade off with plasticity. Does having a variety of genes in the genome provide adaptive advantage in a fluctuating environment and create an optimum individual? Well yes if the environment is changing and they need new ways to survive, but surely there is a cost of carrying around the genetic machinery required to make a plastic response? What do you think?
O’dor RK, Fennel K, Vanden Berghe E. (2009). A one ocean model of biodiversity. Deep-Sea Res Part Ii: Topical Stud Oceanogr 56: 1816–1823.
http://www.sciencedirect.com/science/article/pii/S0967064509001908
Hi Vicky,
ReplyDeletethanks for this detailed response. I have read through O'Dor et al.'s paper and one of the assumptions for their model was that "everything is everywhere" in the Microbial Ocean Realm and that each liter of seawater contains every prokaryotic gene, although at that point this assumption had limited support. So Caporaso et al's findings and the methods they used could provide evidence for the ubiquity of microbes.
So how could this change the way we think about evolution and natural selection? O'Dor et al. (2009) point out that although fitness allows the domination of species by bulking up their biomass and offspring, this may not be the only strategy for long-term survival, particularly if the system changes or single species dominance changes the system. Moreover they change Darwin's "survival of the fittest" to "survival of the stable". Having read some papers on the influence of phylogeny, natural selection usually convincingly offers an explanation about why the physiology or morphology changes over time, but when it comes to how certain traits are conserved in different groups throughout phylogeny, it is more difficult to explain selection for conservation. But as you pointed out, this is very likely due to costs of changing the original machinery. So being stable/conservative could be a more beneficial strategy in the long run, as opposed to investing energy in those new fashionable genes with extra apps and stuff, and to wait till there's something on the market that is truly worth having ;)
Hi Anna,
DeleteThat's a really great analogy you've used - are microbes swapping genes to get the most fashionable apps? :) maybe we should suggest it to Simon for his plasticty letures.
I'm still trying to get my head around this one ocean model, especially the “survival of the stable” because as you said it is more difficult to explain the conservation of traits by natural selection that it is the divergence of traits; in my mind I think I may have put my own spin onto the one ocean model and moved away from what it is really proposing. I just can’t help but think that if everything is everywhere and everything can swap genes then what is there for selection to act on?
Hi
DeleteI see what you mean, how can a force select for individuals with the optimum phenotype if individuals lacking this phenotype can acquire the necessary gene via horizontal gene transfer.. I propose following explanations:
a) horizontal gene transfer is not instant: environmental changes (or the occurence of a predator) take place and in a primary phase individuals with an inapt phenotype are selected against; however, they don't disappear completely and once the right app is on the market (to use the same analogy again) they might acquire it and their abundance will increase again, which brings me to my next point,
b) horizontal gene transfer is not perfect: what is the likelihood that the right gene sequence is available for gene transfer when you need it? and if it's out there, how do you know where to get it from..
c) once again the costs of acquiring new genes is something that we need to consider. Usually apps come with a lot of additional junk information you don't really need and which may interfer with your original machinery
d) and finally maybe the way we think of natural selection in macroscopic organisms is indeed not applicable to microbes. Horizontal gene transfer makes interaction between species far more dynamic and the idea of competition in a world were information is shared between individual of whatever group very vague. Anyway did any bacterial species/ group ever go extinct (extinction being the ultimate results of natural selection)? If so, I think that's where we would find indication about how natural selection acts on bacteria.
I agree plasticity and horizontal transfer should be intimitely linked, would be interesting to discuss this further with Simon.
I have found two interesting reviews, which both address topics we have discussed:
DeleteBoto, L., 2010. Horizontal gene transfer in evolution: facts and challenges. Proceedings. Biological sciences / The Royal Society, 277(1683), pp.819–27.
Harrison, E. & Brockhurst, M. a, 2012. Plasmid-mediated horizontal gene transfer is a coevolutionary process. Trends in microbiology, 20(6), pp.262–7.
The first one looks at HGT and its implications on phylogeny and puts forward the need of a new evolutionary synthesis including HGT.
The second one deals mainly with plasmids and co-evolution and the cost-of-carriage.
Thanks Anna, I'll definitely have a read of those! I've managed to get hold of Theo Garland and Michael Rose's "Experimental Evolution" book and there is a chapter on how microbes and viruses fit into the big picture so I'll let you know how it goes :)
ReplyDelete