Table 3.
An overview on DNA-based methods of fungal samples analyses.
| Global Fungi Study ID | Substrate | Samples | Method | Sequencing Platform | ITS2 Sequences | Reference |
|---|---|---|---|---|---|---|
| Hartmann_2012_B1A3 | – | 6 | Culture independent | 454-pyrosequencing | 2155088 | [150] |
| Ihrmark_2012_3AE5 | Soil, wood, wheat roots and hay | 36 | Culture independent | 454-pyrosequencing | 414896 | [151] |
| Davey_2012_6F6A | Shoots of Hylocomium splendens, Pleurozium schreberi, and Polytrichum commune | 301 | Culture independent | 454-pyrosequencing | 296964 | [152] |
| Peay_2013_74BB | Soil | 36 | Culture independent | 454-pyrosequencing | 86677 | [153] |
| Davey_2013_7683 | Shoots of Dicranum scoparium, Hylocomium splendens, Pleurozium schreberi and Polytrichum commune | 454-pyrosequencing | Culture independent | 454-pyrosequencing | 313084 | [154] |
| Talbot_2014_A187 | Soil | 555 | Culture independent | 454-pyrosequencing | 16977 | [155] |
| Tedersoo_2014_B9DD | Soil | 360 | Culture independent | 454-pyrosequencing | 1979803 | [156] |
| Kadowaki_2014_B85B | Soil | 46 | Culture independent | 454-pyrosequencing | 66067 | [157] |
| Geml_2014_2936 | Soil | 10 | Culture independent | 454-pyrosequencing | 285031 | [158] |
| Davey_2014_2252 | Shoots of Hylocomium splendens | 251 | Culture independent | 454-pyrosequencing | 639746 | [159] |
| McHugh_2015_CAE1 | Soil | 20 | Culture independent | 454-pyrosequencing | 594424 | [160] |
| DeBeeck_2014_14DC | Soil | 20 | Culture independent | 454-pyrosequencing | 32778 | [161] |
| Yamamoto_2014_C3F7 | Seedlings of Quercus sp. | 431 | Culture independent | 454-pyrosequencing | 59021 | [162] |
| Walker_2014_22C1 | Soil | 24 | Culture independent | 454-pyrosequencing | 34267 | [163] |
| Veach_2015_7FDE | Soil | 91 | Culture independent | Illumina MiSeq | 579967 | [164] |
| Zhang_2015_A52F | Seven lichens speciesViz. Cetrariella delisei, Cladonia borealis, C. arbuscula, C. pocillum, Flavocetraria nivalis, Ochrolechia frigida and Peltigera canina | 22 | Culture independent | 454-pyrosequencing | 11087 | [165] |
| Elliott_2015_7CC2 | Soil | 16 | Culture independent | 454-pyrosequencing | 3896 | [166] |
| Geml_2015_1A45 | Soil | 10 | Culture independent | Ion Torrent | 1098472 | [167] |
| Hoppe_2015_BE27 | Wood | 48 | Culture independent | 454-pyrosequencing | 121459 | [168] |
| Jarvis_2015_B613 | Roots of Pinus sylvestris | 32 | Culture independent | 454-pyrosequencing | 112333 | [169] |
| Chaput_2015_41F7 | Soil | 4 | Culture independent | Tag-encoded FLX amplicon pyrosequencing | 1197 | [170] |
| van_der_Wal_2015_1114 | Sawdust from sapwood and heartwood of Quercus robur, Rubus fruticosus, Sorbus aucuparia, Betula pendula, Pteridium aquilinum and Amelanchier lamarckii |
42 | Culture independent | 454-pyrosequencing | 543801 | [171] |
| Clemmensen_2015_B0AE | Soil | 466 | Culture independent | 454-pyrosequencing GL FLX Titanium system | 592836 | [172] |
| Gao_2015_1CEF | Soil | 24 | Culture independent | 454-pyrosequencing GL FLX Titanium system | 93683 | [173] |
| Liu_2015_6174 | Soil | 26 | Culture independent | Roche FLX 454- pyrosequencing | 53978 | [174] |
| Oja_2015_88D4 |
Cypripedium calceolus (subfamily Cypripedioideae), Neottia ovata
(Epidendroideae) and Orchis militaris (Orchidoideae) and Soil |
158 | Culture independent | 454-pyrosequencing | 63045 | [175] |
| Goldmann_2015_EA26 | Soil | 48 | Culture independent | 454-pyrosequencer | 140966 | [176] |
| Tedersoo_2015_ED81 | Soil | 11 | Culture independent | Illumina MiSeq | 261751 | [177] |
| Rime_2015_89DE | Soil | 36 | Culture independent | 454-pyrosequencing GL FLX Titanium system | 227118 | [178] |
| Sterkenburg_2015_5E14 | Soil | 56 | Culture independent | 454-pyrosequencing | 350560 | [179] |
| Stursova_2016_D385 | Soil | 96 | Culture independent | Illumina MiSeq | 452546 | [180] |
| Semenova_2016_576B | Soil | 10 | Culture independent | Ion Torrent sequencing | 1007509 | [181] |
| Santalahti_2016_74FC | Soil | 117 | Culture independent | 454-pyrosequencing | 739877 | [182] |
| Rime_2016_E0E4 | Soils and sediments | 2 | Culture independent | 454-pyrosequencing | 35937 | [183] |
| RoyBolduc_2016_E50C | Root and soil | 63 | Culture independent | 454-pyrosequencing | 248325 | [184] |
| RoyBolduc_2016_F11B | Soil | 77 | Culture independent | 454-pyrosequencing | 280272 | [185] |
| Tedersoo_2016_TDEF | Soil | 136 | Culture independent | 454-pyrosequencing | 788372 | [186] |
| UOBC_2016_5CA6 | Soil | 655 | Culture independent | Illumina HiSeq | 7138323 | [187] |
| Urbina_2016_CE8E | Soil | 21 | Culture independent | Ion Torrent sequencing | 564332 | [188] |
| Valverde_2016_5E5C | Soil from the rhizosphere of Welwitschia mirabilis | 8 | Culture independent | 454-pyrosequencing | 2677 | [189] |
| Nacke_2016_8F49 | Soil from the rhizosphere Fagus sylvatica and Picea abies | 160 | Culture independent | 454-pyrosequencing | 386432 | [190] |
| Newsham_2016_191B | Soil | 29 | Culture independent | 454-pyrosequencing | 509483 | [191] |
| Nguyen_2016_D8E8 | Shoots of Picea abies, Abies alba, Fagus sylvatica, Acer pseudoplatanus, Fraxinus excelsior, Quercus robur, Pinus sylvestris, Betula pendula, Carpinus betulus and Quercus robur | 221 | Culture independent | 454-pyrosequencing | 63853 | [192] |
| Goldmann_2016_0757 | Root and soil samples from beech-dominated plots | 29 | Culture independent | 454-pyrosequencing | 85867 | [193] |
| Bahram_2016_7246 | Soil | 123 | Culture independent | 454-pyrosequencing | 213249 | [194] |
| Gehring_2016_E395 | Roots and root-associated (rhizosphere) soil of sagebrush, cheatgrass, and rice grass plants | 60 | - | - | 1161117 | [195] |
| Gourmelon_2016_9281 | Soil | 32 | Culture independent | Illumina MiSeq | 91814 | [196] |
| Bissett_AAAA_2016 | Soil | 2061 | Culture independent | Illumina MiSeq | 50810033 | [197] |
| Cox_2016_EDC5 | Soil | 135 | Culture independent | 454-pyrosequencing | 886200 | [198] |
| Oh_2016_DEBA | Soil | 12 | Culture independent | 454-pyrosequencing | 98376 | [199] |
| Frey_2016_5D5C | Soil | 12 | Culture independent | Illumina MiSeq v3 | 500999 | [200] |
| Gannes_2016_5E98 | Soil | 23 | Culture independent | Illumina MiSeq system | 218946 | [201] |
| Li_2016_1EBC | Soil | 21 | Culture independent | Illumina MiSeq system | 129184 | [202] |
| Kielak_2016_1110 | Wood of Pinus sylvestris | 75 | Culture independent | 454-pyrosequencing | 1281356 | [203] |
| Ji_2016_C06E | Soil | 13 | Culture independent | 454-pyrosequencing | 277 | [204] |
| Baldrian_2016_DE02 | Sawdust | 118 | Culture independent | llumina MiSeq | 1205580 | [205] |
| Barnes_2016_0042 | Roots of Cinchona calisaya | 21 | Culture independent | llumina MiSeq | 239387 | [206] |
| Porter_2016_CD8D | Soil | 2 | Culture independent | 454-pyrosequencing | 20123 | [207] |
| Zhou_2016_A8F1 | Soil | 126 | Culture independent | Illumina MiSeq | 3542416 | [208] |
| Zhang_2016_1DA0 | Soil | 13 | Culture independent | 454-pyrosequencing | 2362 | [209] |
| Wang_2016_6223 | Roots, stems, and sprouts of rice plant | 1 | Culture independent | Illumina MiSeq | 1850 | [210] |
| Zifcakova_2016_4C03 | Soil | 24 | Culture independent | ILLUMINA HISEQ2000 |
123869 | [211] |
| VanDerWal_2016_4C9C | Sawdust from sapwood and heartwood | 130 | Culture independent | 454-pyrosequencing | 1215932 | [212] |
| Varenius_2017_BCFB | Soil | 517 | Culture independent | PacBio RSII platform by SciLifeLab | 186474 | [213] |
| van_der_Wal_2017_2D0D | Sawdust samples of Larix stumps, and Quercus stumps | 88 | Culture independent | Illumina MiSeq | 877425 | [214] |
| Wang_2017_7E18 | Soil | 6 | Culture independent | 454-pyrosequencing | 53737 | [215] |
| van_der_Wal_2017_3070 | Soil | 135 | Culture independent | Illumina MiSeq | 1572834 | [216] |
| Vasutova_2017_3070 | Soil | 28 | Culture independent | GS Junior sequencer |
9370 | [217] |
| Vaz_2017_C16E | Woody debris | 2 | Culture independent | Personal Genome Machine | 11817 | [218] |
| Yang_2017_2AFC | Soil | 180 | Culture independent | llumina MiSeq platform PE250 | 12688168 | [219] |
| Wicaksono_2017_3B9E | Root samples of Alnus acuminata | 24 | Culture independent | Ion Torrent | 3596531 | [220] |
| Yang_2017_EB1D | Soil | 26 | Culture independent | Illumina MiSeq platform PE250 |
1450233 | [221] |
| Zhang_2017_02C2 | Plant litter and soil | 54 | Culture independent | Illumina MiSeq | 2904476 | [222] |
| Zhang_2017_F933 | Peat soil | 9 | Culture independent | Illumina HiSeq2000 | 320199 | [223] |
| Purahong_2017_8EFD | Wood sample | 116 | Culture independent | Genome Sequencer 454-FLX System | 299831 | [224] |
| Poosakkannu_2017_B342 | Bulk soil, rhizosphere soil, and D. flexuosa Leaf | 43 | Culture independent | IonTorrent | 259743 | [225] |
| Bergottini_2017_02C2 | Roots of Ilex paraguariensis | 11 | Culture independent | 454-pyrosequencing | 189048 | [226] |
| Dean_2017_F5A5 | Roots of Glycine max (soybean) and Thlaspi arvense | 12 | Culture independent | 454-FLX titanium | 12596 | [227] |
| Fernandez_Martinez_2017_14C3 | Soil | 11 | Culture independent | 454-pyrosequencing | 138524 | [228] |
| Ge_2017_4DC8 | Roots of Quercus nigra, Q. virginiana, Q. laevis, Carya cf. glabra, Carya cf. tomentosa as well as several Carya and Quercus spp. | 9 | Culture independent | 454-pyrosequencing | 44 | [229] |
| Gomes_2017_2AFC | Roots of Thismia sp. | 61 | Culture independent | Ion Torrent | 4067438 | [230] |
| Almario_2017_2082 | Root and rhizosphere of Arabis alpina | 26 | Culture independent | Illumina Miseq | 805679 | [231] |
| Anthony_2017_647F | Soil | 142 | Culture independent | Illumina Miseq | 12453259 | [232] |
| Grau_2017_E29A | Soil | 27 | Culture independent | Ion Torrent | 960177 | [233] |
| Hiiesalu_2017_E29A | Soil | 1 | Culture independent | 454-pyrosequencing | 4616 | [234] |
| Nguyen_2017_6F2C | Leaf samples of Betula pendula | 20 | Culture independent | 454-pyrosequencing | 1318 | [235] |
| Kolarikova_2017_EB1D | Roots of Salix caprea and Betula pendula | 24 | Culture independent | 454-pyrosequencing | 47543 | [236] |
| Kyaschenko_2017_89D4 | Soil | 30 | Culture independent | PacBio sequencing | 64010 | [237] |
| Oja_2017_AD29 | Roots and rhizosphere soil of | 333 | Culture independent | 454-pyrosequencing | 446296 | [238] |
| Miura_2017_2BE5 | Leaves and berries of grapes | 36 | Culture independent | Illumina MiSeq | 2250530 | [239] |
| Oono_2017_B342 | Needles of Pinus taeda | 143 | Culture independent | Illumina MiSeq | 9755183 | [240] |
| Kamutando_2017_6F2C | Soil | 3 | Culture independent | Illumina MiSeq | 4 | [241] |
| Shen_2017_C7F4 | Soil | 1 | Culture independent | Illumina MiSeq | 1 | [242] |
| Smith_2017_2AFC | Root of Dicymbe corymbosa | 8 | Culture independent | 454-pyrosequencing | 94 | [243] |
| Tian_2017_F933 | Soil | 3 | Culture independent | 454-GS FLX+pyrosequencing machine | 25001 | [244] |
| Tu_2017_BCFB | Soil | 60 | Culture independent | Illumina MiSeq | 696557 | [245] |
| Sharma_Poudyal_2017_F933 | Soil | 53 | Culture independent | 454-FLX titanium | 7680 | [246] |
| Cross_2017_2AFC | Leaflet, petiole upper and petiole base tissues of ash leaves of Fraxinus excelsior (common ash) | 27 | Culture independent | 454-pyrosequencing | 171094 | [247] |
| Kazartsev_2018_1115 | Bark of Picea abies | 20 | Culture independent | 454-pyrosequencing | 22918 | [248] |
| Bickford_2018_2EE0 | Roots of Phragmites spp. | 3 | Culture independent | PacBio-RS II | 66439 | [249] |
| Cline_2018_0BCC | Wood of Betula papyrifera | 15 | Culture independent | 454-FLX titanium | 660 | [250] |
| Cregger_2018_added | Roots, stems, and leaves of Populus deltoides and the Populus trichocarpa × deltoides hybrid | 290 | Culture independent | Illumina MiSeq | 14767409 | [251] |
| Marasco_2018_DBE1 | Rhizosheath-root system of Stipagrostis sabulicola, S. seelyae and Cladoraphis spinosa | 49 | Culture independent | Illumina MiSeq | 4694085 | [252] |
| Glynou_2018_445A | Roots of nonmycorrhizal Microthlaspi spp. | 5 | Culture independent | Illumina Miseq | 7 | [253] |
| Montagna_2018_E316 | Soil | 24 | Culture independent | Illumina Miseq | 2475767 | [254] |
| Schlegel_2018_A231 | Leaves of Fraxinus spp. and Acer pseudoplatanus | 353 | Culture independent | Illumina MiSeq | 24198214 | [255] |
| SchneiderMaunoury_2018_51AB | Different plant species | 78 | Culture independent | Ion Torrent | 352332 | [256] |
| Schon_2018_01F4 | Soil | 18 | Culture independent | Illumina MiSeq | 235709 | [257] |
| Rasmussen_2018_C8E6 | Root samples | 228 | Culture independent | Illumina MiSeq | 428044 | [258] |
| Rogers_2018_147F | Hemlock stems | 6 | Culture independent | Illumina MiSeq | 675067 | [259] |
| Purahong_2018_14C0 | Deadwood logs | 297 | Culture independent | 454-pyrosequencing | 2034928 | [260] |
| Qian_2018_2B1E | Leaves of Mussaenda shikokiana | 20 | Culture independent | Illumina MiSeq | 449179 | [261] |
| Park_2018_569C | Calanthe species: C. aristulifera, C. bicolor, C. discolor, C. insularis and C. striata | 12 | Culture independent | 454-GS FLX +System | 65867 | [262] |
| Mirmajlessi_2018_765D | Soil | 40 | Culture independent | Illumina MiSeq | 1077125 | [263] |
| Purahong_2018_9F2E | Wood samples | 96 | Culture independent | 454-pyrosequencing | 656682 | [264] |
| Si_2018_53B6 | Soil | 27 | Culture independent | Illumina MiSeq | 692169 | [265] |
| Saitta_2018_51C8 | Soil | 16 | Culture independent | Illumina MiSeq | 4923667 | [266] |
| Santalahti_2018_3794 | Soil | 38 | Culture independent | 454-pyrosequencing | 218387 | [267] |
| Sukdeo_2018_1DF4 | Soil | 126 | Culture independent | Illumina MiSeq | 32336646 | [268] |
| Zhu_2018_1E38 | Soil | 12 | Culture independent | Illumina MiSeq | 1031479 | [269] |
| Zhang_2018_F81F | Soil | 106 | Culture independent | Illumina HiSeq | 1673070 | [270] |
| Zhang_2018_491A | Bare sand, algal crusts, lichen crusts, and moss crusts | 17 | Culture independent | Illumina Miseq | 442056 | [271] |
| Sun_2018_1B01 | Soil | 36 | Culture independent | Illumina Miseq | 1188520 | [272] |
| Weissbecker_2019_6A75 | Soil | 394 | Culture independent | GS-FLX + 454 pyrosequencer | 1109208 | [273] |
| Purahong_AD_2019 | Wood chips of rotted heartwood deadwood from C. carlesii | 3 | Culture independent | PacBio RS II system | 22886 | [274] |
| Egidi_AD_2019 | Soil | 161 | Culture independent | Illumina MiSeq | 14131987 | [275] |
| Froeslev_2019_CA74 | Soil | 276 | Culture independent | Illumina MiSeq | 6114124 | [276] |
| Ogwu_2019_38FE | Soil | 13 | Culture independent | Illumina Miseq | 724483 | [277] |
| Ovaskainen_2019_air | Soil particles, spores, pollen, bacteria, and small insects | 75 | Culture independent | Illumina Miseq | 935812 | [278] |
| Qian_2019_9691 | Leaves and soil | 30 | Culture independent | Illumina HiSeq | 2133292 | [279] |
| Ramirez_2019_D0B2 | Soil | 810 | Culture independent | Illumina Miseq | 6555903 | [280] |
| Pellitier_2019_82BC | Bark of black oak (Quercus velutina), white oak (Q. alba), red pine (Pinus resinosa), eastern white pine (P. strobus) and red maple (Acer rubrum) | 15 | Culture independent | Illumina MiSeq | 10649956 | [281] |
| Semenova-Nelsen_2019_add | Litter and the uppermost soil | 121 | Culture independent | Illumina MiSeq | 3205748 | [282] |
| Sheng_2019_66AC | Soil | 16 | Culture independent | Illumina MiSeq | 447840 | [283] |
| Shigyo_2019_5B19 | Soil | 144 | Culture independent | Illumina MiSeq | 4353704 | [284] |
| Schroter_2019_1B64 | Fine roots and soil | 3 | Culture independent | Roche GS-FLX+ pyrosequencer | 144 | [285] |
| Singh_2019_EA7F | Fine roots and soil | 96 | Culture independent | Illumina MiSeq | 3138303 | [286] |
| Song_2019_ad2 | Soil | 46 | Culture independent | Illumina MiSeq | 920391 | [287] |
| U’Ren_2019_add | Fresh, photosynthetic tissues of a diverse range of plants and lichens |
486 | Culture-based sampling and culture-independent | Illumina MiSeq | 5671834 | [288] |
| Unuk_2019_567A | Fine roots and soil | 30 | Culture independent | Ilumina MiSeq | 470786 | [289] |
| Araya_2019_add | Soil | 36 | Culture independent | Illumina MiSeq | 8083471 | [290] |
| Alvarez-Garrido_2019_add | Root tips from A. pinsapo trees following the trunk to the superficial secondary roots | 76 | Culture independent | Illumina MiSeq | 1795423 | [291] |
| Wei_2019_3796 | Soil | 1 | Culture independent | Illumina HiSeq | 18 | [292] |
| Pan_2020_addZ | Soil from the rhizosphere of potato | 1 | Culture independent | Illumina MiSeq | 2 | [293] |
| Detheridge_2020_Z | Soil | 70 | Culture independent | 1832454 | [294] | |
| Li_2020_AS | Soil | 19 | Culture independent | Illumina MiSeq | 116660 | [295] |