Ecological Significance of Microdiversity: Identical 16S rRNA Gene
Sequences Can Be Found in Bacteria with Highly Divergent
Genomes and Ecophysiologies
Elke Jaspers and [Jo¨rg] Overmann
Applied and Environmental Microbiology, Aug. 2004, p. 4831–4839
Major Issue:
The conclusion of this paper can be read in the title. It really isn't all that complicated, nor is it unexpected to any evolutionary biologist.
Basically, the 16S rRNA doesn't change very fast, and changes are discrete and rather random, and some changes demand compensatory changes. So, all this being said, there is going to come a time when the rRNA fakes right while the rest of the genome is running left, and you'll end up with an incongruity in the phylogenies at a small scale, maybe at the level of genera or something. This could of course be massaged out of the data if we knew how to weight various parts of the 16S sequence, but we use this data precisely because we don't know how, and we daren't use other housekeeping genes for broad phylogenies.
In essence, we are depending on something that indicates gross phylogenetic position to do too fine a scale phylogenies because we are ignorant of the details within these various clades.
On top of this, we tend to use phylogeny as a proxy for all sorts of taxonomy, including ecological functional taxonomy. Everyone knows that this is purely a convenient, slapdash way to do things. After all, just thinking about ecology in general, plants, bacteria and fungi can all serve as primary producers. Protozoa and bacteria and fungi can serve as detritovores. Fungi, protozoa and plants can be predators at the micro level. It goes on. Phylogeneny has little to say about broad ecological roles. On the opposite end, we know that many pathogens are closely related to symbiotes, but have a very different lifestyle because of a small cluster of genes. Similarly, apes and humans function very differently in the ecology. Even black and white rhinos are very different, because one eats grasses, the other shrubs.
So, all in all, this conclusion that the 16S doesn't represent phylogeny frequently, and further that it doesn't represent ecology, should not surprise us. What is sad is that many people pretend as if it does. They get a whole bunch of 16S sequences out of an environmental sample and make bold statements about how many sulfer reducers and how many this and that are in the environmental sample.
Ignorng the paper's somewhat controversial use of 'ecotype' language, the result that they have put forward should thus is nothing more than revealing the emporer's new clothes in certain aspects of molecular ecology. While everyone is busy trumpeting PCR bias and DNA recovery biases, the very use of 16S rRNA to characterize communities is a dreadfully inadequate shorthand, and even if done perfectly says very little without systematically confirming the identity of the various 16S rRNA bearing strains, making sure there is a 1-to-1 correlation between the sequences and the strains (or species) and their ecological functions.
In the current environment, this sort of research seems hardly practical - which leads us back to an impasse. 16S rRNA is great at telling us something about the bugs, but not good at telling us much about them. A fingerprint of a community is likely to help us highlight when a major change occured, simply because major changes that compensate for other ones in the fingerprint should be very rare, but it tells us relatively little about who disappeared, or what replaced them.
For anyone relying too much on 16S rRNA in microbial ecology, this should be a scary paper. It points to the continued need for specialists at he organismal level in the various clades, people who can use other genes, specially functional enzymes under selective pressures, to identify what is going on in an environment.
Sequences Can Be Found in Bacteria with Highly Divergent
Genomes and Ecophysiologies
Elke Jaspers and [Jo¨rg] Overmann
Applied and Environmental Microbiology, Aug. 2004, p. 4831–4839
Major Issue:
The conclusion of this paper can be read in the title. It really isn't all that complicated, nor is it unexpected to any evolutionary biologist.
Basically, the 16S rRNA doesn't change very fast, and changes are discrete and rather random, and some changes demand compensatory changes. So, all this being said, there is going to come a time when the rRNA fakes right while the rest of the genome is running left, and you'll end up with an incongruity in the phylogenies at a small scale, maybe at the level of genera or something. This could of course be massaged out of the data if we knew how to weight various parts of the 16S sequence, but we use this data precisely because we don't know how, and we daren't use other housekeeping genes for broad phylogenies.
In essence, we are depending on something that indicates gross phylogenetic position to do too fine a scale phylogenies because we are ignorant of the details within these various clades.
On top of this, we tend to use phylogeny as a proxy for all sorts of taxonomy, including ecological functional taxonomy. Everyone knows that this is purely a convenient, slapdash way to do things. After all, just thinking about ecology in general, plants, bacteria and fungi can all serve as primary producers. Protozoa and bacteria and fungi can serve as detritovores. Fungi, protozoa and plants can be predators at the micro level. It goes on. Phylogeneny has little to say about broad ecological roles. On the opposite end, we know that many pathogens are closely related to symbiotes, but have a very different lifestyle because of a small cluster of genes. Similarly, apes and humans function very differently in the ecology. Even black and white rhinos are very different, because one eats grasses, the other shrubs.
So, all in all, this conclusion that the 16S doesn't represent phylogeny frequently, and further that it doesn't represent ecology, should not surprise us. What is sad is that many people pretend as if it does. They get a whole bunch of 16S sequences out of an environmental sample and make bold statements about how many sulfer reducers and how many this and that are in the environmental sample.
Ignorng the paper's somewhat controversial use of 'ecotype' language, the result that they have put forward should thus is nothing more than revealing the emporer's new clothes in certain aspects of molecular ecology. While everyone is busy trumpeting PCR bias and DNA recovery biases, the very use of 16S rRNA to characterize communities is a dreadfully inadequate shorthand, and even if done perfectly says very little without systematically confirming the identity of the various 16S rRNA bearing strains, making sure there is a 1-to-1 correlation between the sequences and the strains (or species) and their ecological functions.
In the current environment, this sort of research seems hardly practical - which leads us back to an impasse. 16S rRNA is great at telling us something about the bugs, but not good at telling us much about them. A fingerprint of a community is likely to help us highlight when a major change occured, simply because major changes that compensate for other ones in the fingerprint should be very rare, but it tells us relatively little about who disappeared, or what replaced them.
For anyone relying too much on 16S rRNA in microbial ecology, this should be a scary paper. It points to the continued need for specialists at he organismal level in the various clades, people who can use other genes, specially functional enzymes under selective pressures, to identify what is going on in an environment.
posted by BenK at 5:08 PM
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