Plankton Diversity in the Bay of Fundy as Measured by
Morphological and Molecular Methods
M.C. Savin J.L. Martin, M. LeGresley, M. Giewat and J. Rooney-Varga
Microbial Ecology Volume 48, 51–65 (2004)
Basic Problem:
In days of Yore, as they say, you could identify plants and animals by what they looked like. Morphology.
Then came the hordes of rampaging microbiologists, who realized that classifying all bacteria into "rod shaped (long and short), round (clustered this way and that), comma shaped, and spiral" wasn't going to cut it. They started using biochemical tests instead: ferments glucose, produce gas, produces acid from lactose, etc. These biochemical tests often had the virtue of being related to industrial applications or medical purposes (hemolytic, etc). These were called Phenotypic tests. More sophisticated classifications were done with serotyping, which relied on the otherwise difficult to observe phenotypes related to cell surface antigens.
Well, the microbiologists pressed on and on, but meanwhile, algae and plankton had not really ever entered into their sphere of influence, and had remained the domain of botanists. Botanists, used to a wealth of informative morphological characters, just picked up the microscope and kept looking for the shapes of leaves, etc. Luckily for them, algae and diatoms and such had more morphology than bacteria. So, their method was more or less successful at creating some classification system.
Well, this has led to a crisis for plankton taxonomy. With plants and animals, some traits have been deceptive, but many morphological characters have been quite informaitive relative to phylogeny. Microbiologists' tests, as it turns out, bore at least some congruence to the presence and absence of key housekeeping genes and pathways, and led somewhat naturally to the current species conceptions that rely on phylogeny (medically relevant characteristics have had a more difficult transition). While discussing and debating bacterial species could take a several volume monograph, suffice it to say that at least there is some value in continuing to talk about the biochemical tests even if you prefer MLST-based taxonomy.
This paper attempts to discern whether there is any hope at all for the existing morphological taxonomy of plankton to have relevance in the modern ecological and phylogenetic taxonomic frameworks.
The Methods:
The choice of the bay of Fundy is naturally arbitrary. I hope it was convenient, because as a vacation spot it seems lousy. The plankton of Guam, on the other hand, should be fascinating...
Anyway, the morphological examination was done in the standard way, I hope (I can't really tell, not being an expert in plankton). The need to use an SEM to identify your taxa indicates to me that morphology is probably a big pain with these plankton, and that they may not be losing much by having to switch to molecular methods, unlike students of some other fields with more convenient but now outdated taxonomic strategies.
They chose to do a sort of ribotyping (DGGE fingerprint), using the 18S (like the bacterial 16S, a slow but steady, broad-spectrum gene across eukaryotes). They also wanted to do sequencing, but it was apparently difficult and they had to resort to cloning to make it happen. The DGGE typing also allowed them to do a 'quick' sort of community analysis. They used bead beating technology to minimize genomic DNA lysis bias, a good idea.
Their results seem solid if problematic. For one, most of their sequences landed in that no-mans-land of parts of the tree where there are other sequences from unidentified, uncultured, uncharacterized environmental isolates.
Worse, "Very few of the organisms identified by morphology were also identified in phylogenetic analyses." In some sense, this is inexcusable - they ought to have been able to try something like aggregating several cells together, or culturing them, to do 18S. However, that would have been a substantial effort, maybe worthy of another paper altogether. At least it should be possible.
The reverse, finding morphologies for rRNA sequences, is probably impossible. And given the extensive discussion of molecular method's biases, which anyone should keep in mind doing molecular ecology, it is clear that quantitative work with environmental samples like these will be difficult to validate.
It hamstrings the paper, though, that they weren't able to find clones for the morphologies and morphologies for the clones. It is known that the two taxonomies aren't congruent, but one would have expected to at least have sequences for the major morphological types.
All in all, this paper does answer one question: studies done the different ways won't be compatible at all. This is a pretty frustrating result, but it isn't entirely unexpected. Direct counts and molecular methods are frequently at odds.
The question of how to improve this state of affairs. Something has to be done to improve our confidence in molecular methods, make sense of the vast and unweildy data a molecular ecology survey returns, and correlate this all to the morphologies. How to do this... especially for plankton... I'm not at all sure.
Morphological and Molecular Methods
M.C. Savin J.L. Martin, M. LeGresley, M. Giewat and J. Rooney-Varga
Microbial Ecology Volume 48, 51–65 (2004)
Basic Problem:
In days of Yore, as they say, you could identify plants and animals by what they looked like. Morphology.
Then came the hordes of rampaging microbiologists, who realized that classifying all bacteria into "rod shaped (long and short), round (clustered this way and that), comma shaped, and spiral" wasn't going to cut it. They started using biochemical tests instead: ferments glucose, produce gas, produces acid from lactose, etc. These biochemical tests often had the virtue of being related to industrial applications or medical purposes (hemolytic, etc). These were called Phenotypic tests. More sophisticated classifications were done with serotyping, which relied on the otherwise difficult to observe phenotypes related to cell surface antigens.
Well, the microbiologists pressed on and on, but meanwhile, algae and plankton had not really ever entered into their sphere of influence, and had remained the domain of botanists. Botanists, used to a wealth of informative morphological characters, just picked up the microscope and kept looking for the shapes of leaves, etc. Luckily for them, algae and diatoms and such had more morphology than bacteria. So, their method was more or less successful at creating some classification system.
Well, this has led to a crisis for plankton taxonomy. With plants and animals, some traits have been deceptive, but many morphological characters have been quite informaitive relative to phylogeny. Microbiologists' tests, as it turns out, bore at least some congruence to the presence and absence of key housekeeping genes and pathways, and led somewhat naturally to the current species conceptions that rely on phylogeny (medically relevant characteristics have had a more difficult transition). While discussing and debating bacterial species could take a several volume monograph, suffice it to say that at least there is some value in continuing to talk about the biochemical tests even if you prefer MLST-based taxonomy.
This paper attempts to discern whether there is any hope at all for the existing morphological taxonomy of plankton to have relevance in the modern ecological and phylogenetic taxonomic frameworks.
The Methods:
The choice of the bay of Fundy is naturally arbitrary. I hope it was convenient, because as a vacation spot it seems lousy. The plankton of Guam, on the other hand, should be fascinating...
Anyway, the morphological examination was done in the standard way, I hope (I can't really tell, not being an expert in plankton). The need to use an SEM to identify your taxa indicates to me that morphology is probably a big pain with these plankton, and that they may not be losing much by having to switch to molecular methods, unlike students of some other fields with more convenient but now outdated taxonomic strategies.
They chose to do a sort of ribotyping (DGGE fingerprint), using the 18S (like the bacterial 16S, a slow but steady, broad-spectrum gene across eukaryotes). They also wanted to do sequencing, but it was apparently difficult and they had to resort to cloning to make it happen. The DGGE typing also allowed them to do a 'quick' sort of community analysis. They used bead beating technology to minimize genomic DNA lysis bias, a good idea.
Their results seem solid if problematic. For one, most of their sequences landed in that no-mans-land of parts of the tree where there are other sequences from unidentified, uncultured, uncharacterized environmental isolates.
Worse, "Very few of the organisms identified by morphology were also identified in phylogenetic analyses." In some sense, this is inexcusable - they ought to have been able to try something like aggregating several cells together, or culturing them, to do 18S. However, that would have been a substantial effort, maybe worthy of another paper altogether. At least it should be possible.
The reverse, finding morphologies for rRNA sequences, is probably impossible. And given the extensive discussion of molecular method's biases, which anyone should keep in mind doing molecular ecology, it is clear that quantitative work with environmental samples like these will be difficult to validate.
It hamstrings the paper, though, that they weren't able to find clones for the morphologies and morphologies for the clones. It is known that the two taxonomies aren't congruent, but one would have expected to at least have sequences for the major morphological types.
All in all, this paper does answer one question: studies done the different ways won't be compatible at all. This is a pretty frustrating result, but it isn't entirely unexpected. Direct counts and molecular methods are frequently at odds.
The question of how to improve this state of affairs. Something has to be done to improve our confidence in molecular methods, make sense of the vast and unweildy data a molecular ecology survey returns, and correlate this all to the morphologies. How to do this... especially for plankton... I'm not at all sure.
posted by BenK at 11:38 AM
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