The taxonomic databases used by the authors to estimate the numbers of microscopic organisms, such as the fungi, are vastly under representative of the true diversity. This is because these databases mostly include organisms that can be cultured and these represent only a fraction of the known diversity. For example, a recent discovery suggests that these databases might not include representatives of an entire Phylum of the fungi (Jones et al 2011). While the authors acknowledge this, it is not accounted for in the analyses, most likely making the estimate of the total number of species unreasonably low.

The estimate for fungi (611000 +or- 297000) is substantially lower than any estimate by experts that have treated this question during the past two decades. Early estimates of fungal diversity on earth (Hawksworth 1991, 2001) concluded that fungi number around 1.5 million species. Most studies over the past two decades on specific fungal groups, or in specific areas, or revisiting these global diversity estimates, have come to the conclusion that this number is conservative. An attempt to establish a 'lower limit' for fungal diversity settled on 712000 (Schmit & Mueller 2007). Estimates that incorporate the current rate of discovery (not description) from environmental samples put the estimate much higher (e.g. more than 5 million, and this too is considered to be an underestimation of the true diversity (O’Brien et al 2005). Other estimates considering environmental samples are even higher (10-100 million species).

As with all studies that estimate the unknown diversity of life, the estimate of 8.7 million will be revised in time. Perhaps most dramatically so as new taxonomic tools (see Hibbett et al 2011) are being developed to deal with the rapid discovery of the unculturable, microscopic diversity from environmental samples. It will be no surprise if the fungal diversity alone matches, or exceeds, the estimated number of 8.7 million for all organisms.

References
- Hawksworth, D.L., 1991. The fungal dimension of biodiversity: magnitude, significance, and conservation. Mycological Research 95, 641-655.
- Hawksworth, D.L., 2001. The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycological Research 105, 1422-1432.
- Hibbett, D.S., Ohman, A., Glotzer, D., Nuhn, M., Kirk, P., Nilsson, R.H., 2011. Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences. Fungal Biology Reviews 25, 38-47.
- Jones, M.D.M., Forn, I., Gadelha, C., Egan, M.J., Bass, D., Massana, R., Richards, T.A., 2011. Discovery of novel intermediate forms redefines the fungal tree of life. Nature 474, 200–203.
- O'Brien, H.E., Parrent, J.L., Jackson, J.A., Moncalvo, J.-M., Vilgalys, R., 2005. Fungal Community Analysis by Large-Scale Sequencing of Environmental Samples. Appl. Environ. Microbiol. 71, 5544-5550.
- Schmit, J., Mueller, G., 2007. An estimate of the lower limit of global fungal diversity. Biodiversity and Conservation 16, 99-111.