Let's examine this statement a bit. In the study here the authors did a heroic task - they did barcoding for some 9000 individuals. It is impressive, in many ways. But one can only call it a large molecular survey of biodiversity if one thinks biodiversity = plants and animals. If however you include microbes, as of course you should, then this new study is not even remotely the "largest molecular survey of biodiversity." In fact, one could argue that 100s if not 1000s of studies of biodiversity of microbes are "larger" in many ways than this study. In microbial studies 9000 "individuals" are characterized routinely in most studies via the use of collecting DNA from environmental samples and sequencing genes from 100s -1000s to even billions of individual cells in a sample. This is done routinely in both metagenomic work (where one collects DNA from the environment and randomly sequences it) or ribosomal RNA PCR surveys where one collects DNA and then sequences rRNA genes from the sample. Overall, hundreds of microbial studies cover more biodiversity than this one - more species - wider phylogenetic diversity - more samples even.
Should these authors here be discussing microbes? I think so. After all, not only would this give their paper historical context. But it would almost certainly give it scientific context and value since there are hundreds of papers on microbes looking at species richness, biodiversity metrics, and such ((a simple pubmed search found 1357 papers using rRNA PCR and diversity as the query, for example). And since the work here is on mitochondrial DNA there may be even more parallels to microbes than one might think at first blush.
Are microbial studies the same as the barcoding studies being done? No. Many barcoding studies have things like individual voucher specimens and museum collections. And microbial studies frequently have mixed samples like soil or water and DNA. So what. The general point of many of these studies is the same - using molecular data to infer information about species richness, beta diversity, phylogenetic patterns, etc. And for this, studies of microbes long preceded the barcoding approach. And there is a lot of useful literature out there as well as tools, methods and concepts. I for one peruse the barcoding papers to see if there is anything useful there for my work. It would almost certainly be good for the barcoding researchers to check out the microbial literature. And if the leaders in the barcoding arena continue to not mention microbes, well that would be unfortunate.