Let me start with the following statement: I agree that there are still many unknown species out there that have to be characterized. BUT...
Modern DNA sequencing is being extensively used to characterize microbial communities. DNA scientists argue that traditional methods cannot detect all species, as many of these organisms cannot be cultured. What are they detecting that traditional microbiologists cannot detect with culturing and microscopy?
My guess is that they rely on the non-proven fact that one sequece = one organism, especially in environmental DNA surveys, and this inflates richness estimates. Over-estimates are often due to technical errors and the documented existence of very stable extracellular DNA. Besides, many microorganisms will never grow in certain environments. Many microbes have never been cultured because of their specific growth requirements (parasites, mycorrhizal fungi, etc), but their taxonomy and ecology are still well characterized.
As an example, the majority of parasites, mycorrhizal fungi, anaerobic microorganisms, symbionts, etc., will never grow on building surfaces, even if their DNA can be detected on these surfaces.
Worse is when you fuction with OTUs. Besides not knowing whether your OTU is an artifact or an organism, you do not know anything about its theoretical biology and ecology, for example of your OTU is functional in the environment you are characterizing.
The so called "rare biosphere" which appears to be a consistent phenomenon in ALL ecosystems that have been DNA-sequenced makes me be skeptical to the common view one sequence = one organism. A recent report from the American Academy of Microbiology on the rare biosphere (http://academy.asm.org/index.php/general-microbiology/463-rare-biosphere) concludes that:
"We need to know whether the rare biosphere is real, not an artifact of the methods we use to analyse microbial communities".
Any thoughts?
Your question made me curious. As I'm a molecular biologist I don't have any doubts about the commonly accepted statement that 1% of Bacteria are cultureable. Of course, you could improve the techniques to get one or two more percent, but you would never go for the majority.
Thats why all the stuff about DNA begins.
To answer the question at the beginning: molecular biologist detect the majority of organisms in the ecosystem.
If you go for 16S for example, you know how your organisms are related to each other, but not much about their function. Publications dealing with functional genes are now more and more found. The time when many publications came out with only publishing a lot of sequences is over.
A big problem is, of course, that you have a sequence but nothing more. High-throughput sequencing techniques depend very much on a good and reliable database. Otherwise you have to work with OTU. This is the challenging thing and the still open issue.
After applying High-throughput sequencing the doubts about the rare biosphere arraised. To go more in detail: in thousends of seqeunces you always have some, which were detected once. The discussion about so called Singeletons is still a hot topic. Either they belong to very rare biosphere or they are an artifact. Maybe it is also a mixture of both.
But if I uderstood your correctly, you have problems with DNA-based methods in general, not just with the singeltons.
You are not alone (of course not) with your doubts. And thanks to this, from the start of DNA-based methods a lot of tool, procedures, troubleshooters and so on were developed to prove the result or also to disregard new "species" which were just chimeric sequences.
The report you quoted tips in my opinion on that point. I understood it that way, that the accept the rare biosphere, but they want to assure, that it is not an artifact. It is a good article to balance the high expectation of the -omics techniques.
I will end here (even I have some more thoughts in mind) and follow the discussion.
Thank you for this interesting opinion!
Karin, thanks for your answer. The question to your first statement is: Has the other 99% of the bacteria been characterized by any way? I know too little about bacteria. My expertise is on moulds.
These 99% (this numbers differs depending on the habitat, but nevertheless stays high) are characterized by their sequence. With a good phylogenetic tree you can assume their function, for example if they belong to a ammonium-oxidizing group.
A small amount (I cannot guess a percentage) is also characterized in other ways: for example stable isotope probing allows conclusion about the position in the trophic network. Just as one example.Also it is possible, if you know what is in there, to adjust culture-methods to especially isolate the species of interest.
For fungi it is a bit more complicated, as some species can only be distingushed by the ITS-region.
To add to your answer Karin.
Single Cell Genomics is doing a great job at characterising the uncultivated. I highly recommend to read the article published in Nature last year doi:10.1038/nature12352
We have been working towards understanding a thermal habitat that is poorly studied. We begin, even before we "try" to isolate DNA, by looking at our samples with DAPI staining, or scanning and transmission em. We commonly find that many of the organisms stick to each other - spheres, rods, filaments, pleomorphic cells, ultrathin filaments (0.2 µm wide). We try to get a feel for the actual sample by looking carefully, but even with that backup, we rely on both culturing and on sequencing, although we have not gone into the millions of sequences....yet. We are at the beginning stages of characterizing thermal habitats that haven't been examined by more than a few labs. Even with minimal sequencing, we have found some very interesting results from both our sequencing and our direct microscopic observations, including FISH. We use multiple approaches to characterize our habitat and that works for us.
Nice comment on the issue by Lynn J. Rothschild: A microbiologist explodes the myth of the unculturables. Nature 443, 248-249 (21 September 2006)
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