Table 2.
Comparison of fungal species numbers resulted by culture-dependent and -independent methods.
| Culture-independent methods | Substrates | Species by culture | OTU numbers | Ratio | References |
|---|---|---|---|---|---|
| TGGE | Wheat rhizosphere | 30 | 41 | 1.4 | Smit et al. 1999 |
| TGGE | Air | 24 | 20 | 0.8 | Nieguitsila et al. 2007 |
| DGGE | Plant hair roots | 38 | 32 | 0.8 | Bougoure and Cairney 2005 |
| DGGE | Plant hair roots | 22 | 24 | 1.1 | Bougoure and Cairney 2005 |
| DGGE | Plant hair roots | 25 | 30 | 1.2 | Bougoure and Cairney 2005 |
| DGGE | Soil | 71 | 100 | 1.4 | Arenz et al. 2006 |
| DGGE | Soil | 37 | 43 | 1.2 | Malosso et al. 2006 |
| DGGE | Sponge | 14 | 23 | 1.6 | Gao et al. 2008 |
| DGGE | Sponge | 20 | 21 | 1.1 | Gao et al. 2008 |
| DGGE | Acidic soil | 5 | 35–40 | 8 | Cosgrove et al. 2010 |
| DGGE | Neutral soil | 4 | 35–40 | 10 | Cosgrove et al. 2010 |
| DGGE | Deep sea sediment | 19 | 46 | 2.4 | Singh et al. 2012 |
| DGGE | Periglacial soil | 37 | 75 | 2.0 | Rodolfi et al. 2016 |
| DGGE | Dough fermentation starter | 4 | 16 | 4.0 | Li et al. 2016 |
| DGGE | Traditionally prepared dried starters | 19 | 46 | 2.4 | Sha et al. 2018 |
| DGGE | Book | 7 | 24 | 3.4 | Okpalanozie et al. 2018 |
| SSCP | Soil | 21 | 42 | 2.0 | Zachow et al. 2009 |
| SSCP | Ophiocordyceps sinensis | 92 | 118 | 1.3 | Zhang et al. 2010 |
| RFLP | Soil | 29 | 30 | 1.0 | Viaud et al. 2000 |
| RFLP | Mycorrhizal roots | 39 | 156 | 4.0 | Allen et al. 2003 |
| RFLP | Adult date palm | 5 | 13 | 2.6 | Chobba et al. 2013 |
| RFLP | Needle litter | 71 | 122 | 1.7 | Haňáčková et al. 2015 |
| T-RFLP | Soil | 12 | 85 | 7.1 | Lord et al. 2002 |
| T-RFLP | Soil | 12 | 23 (18S) | 1.9 | Lord et al. 2002 |
| 18S ARDRA | Grassland soils | 6 | 18 | 3.0 | Hunt et al. 2004 |
| 18S ARDRA | Grassland soils | 7 | 22 | 3.1 | Hunt et al. 2004 |
| 18S ARDRA | Grassland soils | 8 | 29 | 3.6 | Hunt et al. 2004 |
| ARDRA | Soil | 36 | 67 | 1.9 | Malosso et al. 2006 |
| Sequencing | Soil (Orbiliaceae) | 8 | 18 | 2.3 | Smith and Jaffee 2009 |
| PCR-sequencing | Human gut | 5 | 18 | 3.6 | Gouba et al. 2013 |
| Quantitative PCR | Dust | 35 | 450 | 12.9 | Nonnenmann et al. 2012 |
| RISA | Rice wine wheat Qu | 8 | 5 | 0.6 | Xie et al. 2007 |
| Clone libraries | Human distal gut | 3 | 13 | 4.3 | Scanlan and Marchesi 2008 |
| Clone libraries | Dust | 35 | 394 | 11.3 | Pitkäranta et al. 2008 |
| Clone libraries | Moisture buildings | 33 | 305 | 9.2 | Pitkäranta et al. 2011 |
| Clone libraries | Deep sea sediment | 20 | 39 | 2.0 | Singh et al. 2011 |
| Clone libraries | Root | 153 | 304 | 2.0 | Walker et al. 2011 |
| Clone libraries | Human faecal | 5 | 16 | 3.2 | Hamad et al. 2016 |
| Clone libraries | Epoxy resin | 16 | 25 | 1.6 | Pangallo et al. 2015 |
| Clone libraries | Cheese | 8 | 17 | 2.1 | Šuranská et al. 2016 |
| Pyrosequencing | Grassland | 7 | 74 | 10.6 | Lumini et al. 2010 |
| 454 pyrosequencing | Root | 39 | 312 | 8.0 | Tedersoo et al. 2010 |
| 454 pyrosequencing | Air | 24 | 986 | 41.1 | Adams et al. 2013 |
| 454 pyrosequencing | Soil | 29 | 54 | 1.9 | Hirsch et al. 2013 |
| 454 pyrosequencing | Hydrocarbon-contaminated soils | 49 | 360 | 7.3 | Stefani et al. 2015 |
| 454 pyrosequencing | Plant roots | 41 | 592 | 14.4 | Bourdel et al. 2016 |
| 454 pyrosequencing | Grape must | 5 | 15 | 3.0 | Wang et al. 2015a |
| 454 pyrosequencing | Zea mays | 9 | 60 | 6.7 | Bokati et al. 2016 |
| 454 pyrosequencing | Triticum aestivum | 18 | 248 | 13.8 | Bokati et al. 2016 |
| 454 pyrosequencing | Beer | 18 | 1931 | 107.3 | Takahashi et al. 2015 |
| 454 pyrosequencing | Chicha | 16 | 81 | 5.1 | Mendoza et al. 2017 |
| 454 pyrosequencing | Must | 10 | 387 | 38.7 | David et al. 2014 |
| Illumina MiSeq | Root | 43 | 1168 | 27.2 | Parmar et al. 2018 |
| Illumina MiSeq | Book | 13 | 179 | 13.8 | Kraková et al. 2018 |
| Illumina MiSeq | Leaf | 70 | 597 | 8.5 | Siddique et al. 2017 |
| Illumina MiSeq | Cheese | 9 | 14 | 1.6 | Santos et al. 2017 |
| Illumina MiSeq | Wine | 28 | 254 | 9.1 | Li et al. 2018 |
| Illumina MiSeq | Collembola body | 31 | 896 | 28.9 | Anslan et al. 2016 |
| Illumina MiSeq | Collembola gut | 25 | 667 | 26.7 | Anslan et al. 2016 |
| Illumina MiSeq | Rhizospheric | 43 | 860 | 20.0 | Miao et al. 2016 |
| Illumina MiSeq | Chronic-wound | 17 | 482 | 28.4 | Kalan et al. 2016 |
| Illumina HiSeq2500 | Stems of grapevine | 28 | 59 | 2.1 | Dissanayake et al. 2018 |
| Illumina HiSeq2500 | Museum | 9 | 85 | 9.4 | Liu et al. 2018 |
| Illumina HiSeq2501 | Lake | 398 | 479 | 1.2 | Wahl et al. 2018 |
| Average ratio | 8.8 |