Hey there, 

Recently, in microbial ecology the use of NGS technology has become widely accepted as the norm. And, yes this new technology does lead to an overestimation of species richness per se, but, in order to answer your question clearly. Most microbial ecologist use representative OTUs in order to make some suggestions/conclusions regarding species loss. A change in this the representative OTUs can inform community ecologist about changes in abundance of 'keystone' species and the implications there of. 

I love your question.  I am trying to ask that question myself here in California at http://www.ecoseeds.com/arastradero.html because I am starting with a blank slate of zero native flora understory, only occasional fauna visiting because they have a hard time trying to utilize the 100% weed patch that has covered the State since we exterminated the ecosystem about 100-150 years ago, and when we got rid of the native flora, that caused the associated soil fungi to go mostly extinct.  

I am adding back the flora species by species, and that is helping the native gilled fungi to be able to have a habitat, and have counted six new species in the plot so far, whereas the exotic plant-covered area next to the plot is still fungi-free.    

I would suggest concentrating on counting the macroflora and macrofauna first, because there is so little measurement of the natural world to begin with, so you can get a baseline on a particular date on those numbers.  I would suggest also, surveys on a massive scale, like a 2,000-3,000 mile megatransect, like you can see at http://www.ecoseeds.com/megatransect.html or even photo native vegetation megatransects like at http://www.ecoseeds.com/mega.html.  

Once you do a megatransect, like west or east along the 48 deg. north latitude, at http://www.confluence.org/confluence.php?lat=48&lon=-4.  Outside of tropical forests or boreal forests, it is surprising to see how little of the native understory is left on the entire planet in temperate or subtropical areas.  You may see trees, shrubs, even grasses, but other understory herbaceous plants of non-grass family members are mostly gone in 2014.   

Then a look at the micro-forms of life would be useful, but they are usually dependent on the macroflora being there to support them, so where you find diversity and density of the native plants, you should find quantity and diversity in the micro-world also.

Metagenomics have a problem, it is called extracellular DNA. Today I read in the paper that DNA molecules attached to the outer surface of a space shuttel have survived both space conditions and the entrance into the atmosphere. That means very, very high temperatures. There is a risk that not all OTUs detected with metagenomics are organisms.

Hi Maria

I don't really catch your point, since that DNA obviously came first from a living organism. Do you mean that such DNA can be part of a sequence that has been degraded (and may thus be incomplete and therefore misleading as to the original 'owner')?

Best

Didier

I mean that extracellular microbial DNA does exist in nature, and counting this as living organisms is a big mistake in ecological studies and species estimates. Better to combiine DNA with other methods in order to characterize living/active organisms in ecosystems

Maria,

Could you please provide a link to the paper that mentions that extracellular DNA being included in the analysis. Yes, there are cases where extra cellular DNA molecules can exist outside the cell, but, these are usually fragments and degrade quicker in soil environments . Ever rarely do they become incorporated into the analysis. Besides, culture based methods can only capture less 20% of the microbial diversity in the soil. Hence, there has been a shift to culture independent methods. Furthermore, if one does whole genome sequence, these fragments are missed by the sequencing process.  

Itumeleng, I am at home today. I can provide several references from 2014 on Monday. Here is one for the time being. Klein, D.A. (2007) Microbial communities in nature: A postgenomic perspective, Microbe, 2, 591–595

Thanks Maria.

Have a great weekend 

Dear Andrivon

could you send to me a pdf copy of your article?

Best regards.

Dear Maria Luisa

Which article are you requesting? I wrote nothing specifically on the topic of this question. For the rest, please check the full texts of my papers on the site.

Best regards

Didier

Itumeleng, here are two more references addressing extracellular DNA:

Lindahl B.D. et al. 2013. Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide. New Phytologist 199:288-299.

Taberlet P. et al. 2012. Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies. Molecular Ecology 21:1816-1820.

Very interesting question: I think most conservation biologists might agree that molecular data  "change the numbers that estimate biodiversity", specifically this category of phylogenetic and systematic characters (i.e. DNA markers/genomics) allow robust, repeatable, quantitative phylogeographic and reconstruction.  So by "change" what I mean is potential to "refine", "improve" and "increase resolution" of biodiversity assessments.  However, along the lines of what is stated above, usually we can only assess what is remaining, unless comprehensive baseline studies have been conducted, and / or, ancient or museum samples are available for the pre- versus post-impact comparison.