Research Article |
Corresponding author: Lei Cai ( cail@im.ac.cn ) Corresponding author: Pedro W. Crous ( p.crous@wi.knaw.nl ) Academic editor: Thorsten Lumbsch
© 2020 Lingwei Hou, Margarita Hernández-Restrepo, Johannes Zacharias Groenewald, Lei Cai, Pedro W. Crous.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Hou L, Hernández-Restrepo M, Groenewald JZ, Cai L, Crous PW (2020) Citizen science project reveals high diversity in Didymellaceae (Pleosporales, Dothideomycetes). MycoKeys 65: 49-99. https://doi.org/10.3897/mycokeys.65.47704
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Fungal communities play a crucial role in maintaining the health of managed and natural soil environments, which directly or indirectly affect the properties of plants and other soil inhabitants. As part of a Citizen Science Project initiated by the Westerdijk Fungal Biodiversity Institute and the Utrecht University Museum, which aimed to describe novel fungal species from Dutch garden soil, the diversity of Didymellaceae, which is one of the largest families in the Dothideomycetes was investigated. A preliminary analysis of the ITS and LSU sequences from the obtained isolates allowed the identification of 148 strains belonging to the family. Based on a multi-locus phylogeny of a combined ITS, LSU, rpb2 and tub2 alignment, and morphological characteristics, 20 different species were identified in nine genera, namely Ascochyta, Calophoma, Didymella, Juxtiphoma, Nothophoma, Paraboeremia, Phomatodes, Stagonosporopsis, and Xenodidymella. Several isolates confirmed to be ubiquitous plant pathogens or endophytes were for the first time identified from soil, such as Ascochyta syringae, Calophoma clematidis-rectae, and Paraboeremia litseae. Furthermore, one new genus and 12 novel species were described from soil: Ascochyta benningiorum sp. nov., Didymella degraaffiae sp. nov., D. kooimaniorum sp. nov., Juxtiphoma kolkmaniorum sp. nov., Nothophoma brennandiae sp. nov., Paraboeremia rekkeri sp. nov., P. truiniorum sp. nov., Stagonosporopsis stuijvenbergii sp. nov., S. weymaniae sp. nov., Vandijckomycella joseae gen. nov. et sp. nov., V. snoekiae sp. nov., and Xenodidymella weymaniae sp. nov. From the results of this study, soil was revealed to be a rich substrate for members of Didymellaceae, several of which were previously known only from diseased or apparently healthy plant hosts.
biodiversity, new taxa, Phoma, phylogeny, soil-borne fungi
Due to high plasticity and the capacity to adapt and survive in adverse or unfavourable conditions, fungi are exceedingly successful soil inhabitants (
Didymellaceae is a ubiquitous fungal family including saprobic, endophytic and pathogenic species (
The first paper systematically investigating Didymellaceae species from soil was published by
Didymellaceae species from soil always produce diverse metabolites, some of which can be cytotoxic, including cytochalasin A and B, deoxaphomin, proxiphomin and tenuazonic acid (
The present Citizen Science Project was initiated by the Westerdijk Fungal Biodiversity Institute (WI) and the Utrecht University Museum, aiming to investigate the diversity of fungi in Dutch garden soil collected by children in their home gardens from different regions in the Netherlands (
Protocols for the collection and processing of soil samples are described in
Genomic DNA was extracted using the Wizard® Genomic DNA Purification Kit (Promega, Madison, USA) following the manufacturer’s protocols. Initially, the internal transcribed spacer regions 1 and 2 and 5.8S nuclear ribosomal RNA gene (ITS) and partial large subunit nrDNA (LSU) were amplified using primer pairs ITS5/ITS4 (
Taxon name1 | Strain number2 | Substrate | Country | GenBank Accession numbers3 | |||
---|---|---|---|---|---|---|---|
rpb2 | tub2 | ITS | LSU | ||||
Allophoma cylindrispora | CBS 142453T; FMR 13723 | Human superficial tissue | USA | LT593058 | LT592989 | LN907376 | LT592920 |
Al. nicaraguensis | CBS 506.91T; IMI 215229; PD 91/876 | Coffea sp. | Nicaragua | KT389551 | GU237596 | GU238058 | GU237876 |
Al. piperis | CBS 268.93T; PD 88/720 | Peperomia pereskifolia | The Netherlands | KT389554 | GU237644 | GU238129 | GU237816 |
Al. tropica | CBS 436.75T | Saintpaulia ionantha | Germany | KT389556 | GU237663 | GU238149 | GU237864 |
Ascochyta benningiorum | CBS 144957T; JW 196005 | Garden soil | The Netherlands | MN824606 | MN824755 | MN823432 | MN823581 |
CBS 144958; JW 196023 | Garden soil | The Netherlands | MN824607 | MN824756 | MN823433 | MN823582 | |
JW 196013 | Garden soil | The Netherlands | MN824608 | MN824757 | MN823434 | MN823583 | |
A. boeremae | CBS 372.84T; PD 80/1246 | Pisum sativum | Australia | – | KT389774 | KT389697 | KT389480 |
CBS 373.84; PD 80/1247 | Pisum sativum | Australia | KT389560 | KT389775 | KT389698 | KT389481 | |
A. fabae | CBS 649.71 | Vicia faba | The Netherlands | – | GU237527 | GU237964 | GU237902 |
CBS 524.77 | Phaseolus vulgaris | Belgium | – | GU237526 | GU237963 | GU237880 | |
PD 83/492 | Phaseolus vulgaris | The Netherlands | – | GU237528 | GU237965 | GU237917 | |
A. herbicola | CBS 629.97R; PD 76/1017 | Water | USA | KP330421 | GU237614 | GU238083 | GU237898 |
A. lentis | CBS 370.84; PD 81/783 | Lens culinaris | Unknown | – | KT389768 | KT389691 | KT389474 |
A. medicaginicola var. macrospora | CBS 112.53T | Medicago sativa | USA | – | GU237628 | GU238101 | GU237749 |
CBS 404.65R; IMI 116999 | Medicago sativa | Canada | KP330423 | GU237629 | GU238102 | GU237859 | |
A. nigripycnidia | CBS 116.96T; PD 95/7930 | Vicia cracca | Russia | – | GU237637 | GU238118 | GU237756 |
A. phacae | CBS 184.55T | Phaca alpina | Switzerland | – | KT389769 | KT389692 | KT389475 |
A. pisi | CBS 126.54 | Pisum sativum | The Netherlands | DQ677967 | GU237531 | EU754137 | GU237772 |
CBS 122785T; PD 78/517 | Pisum sativum | The Netherlands | – | GU237532 | GU237969 | GU237763 | |
CBS 122751; ATCC 201620 | Pisum sativum | Canada | EU874867 | KP330388 | KP330444 | KP330432 | |
A. rabiei | CBS 534.65 | Cicer arietinum | India | KP330405 | GU237533 | GU237970 | GU237886 |
CBS 237.37T | Cicer arietinum | Bulgaria | – | KT389773 | KT389696 | KT389479 | |
A. syringae | CBS 545.72 | Syringa vulgaris | The Netherlands | – | KT389777 | KT389700 | KT389483 |
JW 1074 | Garden soil | The Netherlands | MN824605 | MN824754 | MN823431 | MN823580 | |
A. versabilis | CBS 876.97R | Silene sp. | The Netherlands | KT389561 | GU237664 | GU238152 | GU237909 |
A. viciae | CBS 451.68 | Vicia sepium | The Netherlands | KT389562 | KT389778 | KT389701 | KT389484 |
A. viciae-pannonicae | CBS 254.92 | Vicia pannonica | Czech Republic | – | KT389779 | KT389702 | KT389485 |
Boeremia exigua var. heteromorpha | CBS 443.94T | Nerium oleander | Italy | KT389573 | GU237497 | GU237935 | GU237866 |
B. exigua var. populi | CBS 100167T; PD 93/217 | Populus (×)euramericana | The Netherlands | – | GU237501 | GU237939 | GU237707 |
Briansuttonomyces eucalypti | CBS 114879T | Eucalyptus sp. | South Africa | – | KU728595 | KU728519 | KU728479 |
CBS 114887 | Eucalyptus sp. | South Africa | – | KU728596 | KU728520 | KU728480 | |
Calophoma clematidina | CBS 102.66 | Clematis sp. | UK | KT389587 | FJ427099 | FJ515630 | FJ426988 |
CBS 108.79T; PD 78/522 | Clematis sp. | The Netherlands | KT389588 | FJ427100 | FJ515632 | FJ426989 | |
C. clematidis-rectae | JW 179007 | Garden soil | The Netherlands | MN824612 | MN824761 | MN823438 | MN823587 |
CBS 507.63 | Clematis sp. | The Netherlands | KT389589 | FJ515624 | FJ515647 | FJ515606 | |
C. vodakii | CBS 173.53T | Hepatica triloba | Switzerland | – | KT389791 | KT389714 | KT389497 |
Coniothyrium palmarum | CBS 400.71 | Chamaerops humilis | Italy | KT389592 | KT389792 | EU754153 | AY720708 |
Cumuliphoma indica | CBS 654.77T; FMR 15341 | Unknown | India | LT623261 | FJ427153 | GU238122 | FJ427043 |
Cu. omnivirens | CBS 341.86T; FMR 14915 | Phaseolus vulgaris | Belgium | LT62326 | FJ427152 | LT623214 | FJ427042 |
Cu. pneumoniae | CBS 142454T; FMR13739 | Human respiratory tract | USA | LT593063 | LT592994 | LN907392 | LT592925 |
Didymella aeria | CGMCC 3.18353T; LC 7441 | Air | China | KY742137 | KY742293 | KY742205 | KY742051 |
D. aliena | LC 8121 | Pyrus calleryana | Italy | – | KY742295 | KY742207 | KY742053 |
CBS 379.93; PD 82/945 | Berberis sp. | The Netherlands | KP330416 | GU237578 | GU238037 | GU237851 | |
D. americana | CBS 185.85R; PD 80/1191 | Zea mays | USA | KT389594 | FJ427088 | GU237990 | FJ426972 |
D. anserina | CBS 360.84R | Potato flour | The Netherlands | KT389596 | GU237551 | GU237993 | GU237839 |
D. aquatica | CGMCC 3.18349T; LC 5556 | Water | China | KY742140 | KY742297 | KY742209 | KY742055 |
D. arachidicola | CBS 333.75T; ATCC 28333; IMI 386092 | Arachis hypogaea | South Africa | KT389598 | GU237554 | GU237996 | GU237833 |
D. aurea | CBS 269.93T; PD 78/1087 | Medicago polymorpha | New Zealand | KT389599 | GU237557 | GU237999 | GU237818 |
D. bellidis | CBS 714.85R; PD 74/265 | Bellis perennis | The Netherlands | KP330417 | GU237586 | GU238046 | GU237904 |
D. boeremae | CBS 109942T; PD 84/402 | Medicago littoralis cv. harbi | Australia | KT389600 | FJ427097 | GU238048 | FJ426982 |
D. brunneospora | CBS 115.58T; FMR 15745 | Chrysanthemum roseum | Germany | KT389625 | KT389802 | KT389723 | KT389505 |
D. calidophila | CBS 448.83T | Desert soil | Egypt | – | FJ427168 | GU238052 | FJ427059 |
D. chenopodii | CBS 128.93R; PD 79/140 | Chenopodium quinoa cv. sajana | Peru | KT389602 | GU237591 | GU238055 | GU237775 |
D. chloroguttulata | CGMCC 3.18351T; LC 7435 | Air | China | KY742142 | KY742299 | KY742211 | KY742057 |
D. coffeae-arabicae | CBS 123380T; PD 84/1013 | Coffea arabica | Ethiopia | KT389603 | FJ427104 | GU238005 | FJ426993 |
D. dactylidis | CBS 124513T; PD 73/1414 | Dactylis glomerata | USA | – | GU237599 | GU238061 | GU237766 |
D. degraaffiae | CBS 144956T; JW 195004 | Garden soil | The Netherlands | MN824470 | MN824618 | MN823295 | MN823444 |
D. dimorpha | CBS 346.82T | Opuntia phyllocladium | Spain | – | GU237606 | GU238068 | GU237835 |
D. ellipsoidea | CGMCC 3.18350T; LC 7434 | Air | China | KY742145 | KY742302 | KY742214 | KY742060 |
D. eucalyptica | CBS 377.91R; PD 79/210 | Eucalyptus sp. | Australia | KT389605 | GU237562 | GU238007 | GU237846 |
D. exigua | CBS 183.55T | Rumex arifolius | France | EU874850 | GU237525 | EU754155 | GU237794 |
D. gardeniae | CBS 626.68T; IMI 108771 | Gardenia jasminoides | India | KT389606 | FJ427114 | GQ387595 | FJ427003 |
D. glomerata | CBS 528.66R; PD 63/590 | Chrysanthemum sp. | The Netherlands | GU371781 | FJ427124 | EU754184 | FJ427013 |
D. heteroderae | CBS 109.92T; PD 73/1405 | Undefined food material | The Netherlands | KT389601 | FJ427098 | GU238002 | FJ426983 |
D. ilicicola | CGMCC 3.18355T; LC 8126 | Ilex chinensis | Italy | KY742150 | KY742307 | KY742219 | KY742065 |
D. infuscatispora | CGMCC 3.18356T; LC 8128 | Chrysanthemum indicum | China | KY742152 | KY742309 | KY742221 | KY742067 |
D. keratinophila | CBS 143032T; FMR 13690 | Human superficial tissue | USA | LT593039 | LT592970 | LN907343 | LT592901 |
D. kooimaniorum | CBS 144951T; JW 27006 | Garden soil | The Netherlands | MN824474 | MN824622 | MN823299 | MN823448 |
D. lethalis | CBS 103.25 | Unknown | Unknown | KT389607 | GU237564 | GU238010 | GU237729 |
D. macrophylla | CGMCC 3.18357T; LC 8131 | Hydrangea macrophylla | Italy | KY742154 | KY742312 | KY742224 | KY742070 |
D. macrostoma | JW 57015 | Garden soil | The Netherlands | MN824472 | MN824620 | MN823297 | MN823446 |
CBS 223.69R | Acer pseudoplatanus | Switzerland | KT389608 | GU237623 | GU238096 | GU237801 | |
JW 149014 | Garden soil | The Netherlands | MN824473 | MN824621 | MN823298 | MN823447 | |
CBS 482.95 | Larix decidua | Germany | KT389609 | GU237626 | GU238099 | GU237869 | |
D. maydis | CBS 588.69T | Zea mays | USA | GU371782 | FJ427190 | EU754192 | FJ427086 |
D. microchlamydospora | CBS 105.95T | Eucalyptus sp. | UK | KP330424 | FJ427138 | GU238104 | FJ427028 |
D. molleriana | CBS 229.79R | Digitalis purpurea | New Zealand | KP330418 | GU237605 | GU238067 | GU237802 |
D. negriana | CBS 358.71R | Vitis vinifera | Germany | KT389610 | GU237635 | GU238116 | GU237838 |
D. nigricans | CBS 444.81T; PDDCC 6546 | Actinidia chinensis | New Zealand | – | GU237558 | GU238000 | GU237867 |
PD 77/919 | Actinidea chinensis | Unknown | – | GU237559 | GU238001 | GU237915 | |
D. ocimicola | CGMCC 3.18358T; LC 8137 | Ocimum sp. | China | – | KY742320 | KY742232 | KY742078 |
D. pedeiae | CBS 124517T; PD 92/612A | Schefflera elegantissima | The Netherlands | KT389612 | GU237642 | GU238127 | GU237770 |
D. pinodella | LC 8139 | Acer palmatum | Japan | KY742161 | KY742322 | KY742234 | KY742080 |
CBS 531.66 | Trifolium pratense | USA | KT389613 | FJ427162 | GU238017 | FJ427052 | |
D. pinodes | CBS 525.77T | Pisum sativum | Belgium | KT389614 | GU237572 | GU238023 | GU237883 |
D. pomorum | JW 196022 | Garden soil | The Netherlands | MN824469 | MN824617 | MN823294 | MN823443 |
CBS 539.66R; IMI 122266; PD 64/914 | Polygonum tataricum | The Netherlands | KT389618 | FJ427166 | GU238028 | FJ427056 | |
D. protuberans | CBS 381.96T; PD 71/706 | Lycium halifolium | The Netherlands | KT389620 | GU237574 | GU238029 | GU237853 |
D. pteridis | CBS 379.96T | Pteris sp. | The Netherlands | KT389624 | KT389801 | KT389722 | KT389504 |
D. rhei | CBS 109177R; PD 2000/9941 | Rheum rhaponticum | New Zealand | KP330428 | GU237653 | GU238139 | GU237743 |
D. rumicicola | CBS 683.79T | Rumex obtusifolius | New Zealand | KT389622 | KT389800 | KT389721 | KT389503 |
CBS 179.97 | Rumex hydrolapathum | The Netherlands | KP330415 | GU237575 | GU238034 | GU237793 | |
CBS 539.77 | Rumex obtusifolius | New Zealand | MN824471 | MN824619 | MN823296 | MN823445 | |
D. sancta | CBS 281.83T | Ailanthus altissima | South Africa | KT389623 | FJ427170 | GU238030 | FJ427063 |
D. segeticola | CGMCC 3.17489T; LC 1636 | Cirsium segetum | China | KP330414 | KP330399 | KP330455 | KP330443 |
D. senecionicola | CBS 160.78R | Senecio jacobaea | New Zealand | – | GU237657 | GU238143 | GU237787 |
D. subglomerata | CBS 110.92R; PD 76/1010 | Triticum sp. | USA | KT389626 | FJ427186 | GU238032 | FJ427080 |
D. subherbarum | CBS 250.92T; PD 92/371 | Zea mays | Canada | – | GU237659 | GU238145 | GU237809 |
D. suiyangensis | CGMCC 3.18352T; LC 7439 | Air | China | KY742169 | KY742332 | KY742244 | KY742090 |
D. viburnicola | CBS 523.73R; PD 69/800 | Viburnum cassioides | The Netherlands | KP330430 | GU237667 | GU238155 | GU237879 |
Ectophoma multirostrata | CBS 274.60T; FMR 15335; IMI 081598 | Soil | India | LT623265 | FJ427141 | GU238111 | FJ427031 |
Ec. pomi | CBS 267.92T; FMR 15346; PD 76/1014 | Coffea arabica | India | LT623263 | GU237643 | GU238128 | GU237814 |
Epicoccum nigrum | CBS 173.73T; IMI 164070 | Dactylis glomerata | USA | KT389632 | FJ427107 | GU237975 | FJ426996 |
LC 8157 | Ocimum sp. | China | KY742179 | KY742352 | KY742264 | KY742110 | |
LC 5180 | Lonicera japonica | China | KY742178 | KY742351 | KY742263 | KY742109 | |
LC 8158 | Poa annua | USA | KY742180 | KY742353 | KY742265 | KY742111 | |
Ep. pimprinum | CBS 246.60T; IMI 081601 | Soil | India | – | FJ427159 | GU237976 | FJ427049 |
PD 77/1028 | Unknown | Unknown | KT389633 | FJ427160 | GU237977 | FJ427050 | |
Heterophoma sylvatica | CBS 874.97T; PD 93/764 | Melampyrum pratense | The Netherlands | – | GU237662 | GU238148 | GU237907 |
H. verbascicola | CGMCC 3.18364T; LC 8163 | Verbascum thapsus | China | KY742187 | KY742361 | KY742273 | KY742119 |
Juxtiphoma eupyrena | JW 164001 | Garden soil | The Netherlands | MN824541 | MN824689 | MN823366 | MN823515 |
JW 263011 | Garden soil | The Netherlands | MN824542 | MN824690 | MN823367 | MN823516 | |
JW 158007 | Garden soil | The Netherlands | MN824543 | MN824691 | MN823368 | MN823517 | |
JW 201014 | Garden soil | The Netherlands | MN824544 | MN824692 | MN823369 | MN823518 | |
JW 213001 | Garden soil | The Netherlands | MN824545 | MN824693 | MN823370 | MN823519 | |
JW 201009 | Garden soil | The Netherlands | MN824546 | MN824694 | MN823371 | MN823520 | |
JW 4005 | Garden soil | The Netherlands | MN824547 | MN824695 | MN823372 | MN823521 | |
JW 4017 | Garden soil | The Netherlands | MN824548 | MN824696 | MN823373 | MN823522 | |
JW 3015 | Garden soil | The Netherlands | MN824549 | MN824697 | MN823374 | MN823523 | |
JW 224006 | Garden soil | The Netherlands | MN824550 | MN824698 | MN823375 | MN823524 | |
JW 132015 | Garden soil | The Netherlands | MN824551 | MN824699 | MN823376 | MN823525 | |
Juxtiphoma eupyrena | JW 146002 | Garden soil | The Netherlands | – | MN824700 | MN823377 | MN823526 |
JW 160021 | Garden soil | The Netherlands | MN824552 | MN824701 | MN823378 | MN823527 | |
JW 18016 | Garden soil | The Netherlands | MN824553 | MN824702 | MN823379 | MN823528 | |
JW 40009 | Garden soil | The Netherlands | MN824554 | MN824703 | MN823380 | MN823529 | |
JW 40019 | Garden soil | The Netherlands | MN824555 | MN824704 | MN823381 | MN823530 | |
JW 97009 | Garden soil | The Netherlands | MN824556 | MN824705 | MN823382 | MN823531 | |
JW 96020 | Garden soil | The Netherlands | MN824557 | MN824706 | MN823383 | MN823532 | |
JW 57007 | Garden soil | The Netherlands | MN824558 | MN824707 | MN823384 | MN823533 | |
JW 149010 | Garden soil | The Netherlands | MN824559 | MN824708 | MN823385 | MN823534 | |
JW 74008 | Garden soil | The Netherlands | MN824560 | MN824709 | MN823386 | MN823535 | |
JW 247003 | Garden soil | The Netherlands | MN824561 | MN824710 | MN823387 | MN823536 | |
JW 267005 | Garden soil | The Netherlands | MN824562 | MN824711 | MN823388 | MN823537 | |
JW 261008 | Garden soil | The Netherlands | MN824563 | MN824712 | MN823389 | MN823538 | |
JW 30012 | Garden soil | The Netherlands | MN824564 | MN824713 | MN823390 | MN823539 | |
JW 167015 | Garden soil | The Netherlands | MN824565 | MN824714 | MN823391 | MN823540 | |
JW 221022B | Garden soil | The Netherlands | MN824566 | MN824715 | MN823392 | MN823541 | |
JW 259004 | Garden soil | The Netherlands | MN824567 | MN824716 | MN823393 | MN823542 | |
JW 73004 | Garden soil | The Netherlands | MN824568 | MN824717 | MN823394 | MN823543 | |
JW 170018 | Garden soil | The Netherlands | MN824569 | MN824718 | MN823395 | MN823544 | |
JW 141018 | Garden soil | The Netherlands | MN824570 | MN824719 | MN823396 | MN823545 | |
JW 181003 | Garden soil | The Netherlands | MN824571 | MN824720 | MN823397 | MN823546 | |
JW 289013 | Garden soil | The Netherlands | MN824572 | MN824721 | MN823398 | MN823547 | |
JW 127004 | Garden soil | The Netherlands | MN824573 | MN824722 | MN823399 | MN823548 | |
JW 81007 | Garden soil | The Netherlands | MN824574 | MN824723 | MN823400 | MN823549 | |
JW 182002 | Garden soil | The Netherlands | MN824575 | MN824724 | MN823401 | MN823550 | |
JW 212001 | Garden soil | The Netherlands | MN824576 | MN824725 | MN823402 | MN823551 | |
JW 191036 | Garden soil | The Netherlands | MN824577 | MN824726 | MN823403 | MN823552 | |
JW 221020 | Garden soil | The Netherlands | MN824578 | MN824727 | MN823404 | MN823553 | |
JW 96002 | Garden soil | The Netherlands | MN824579 | MN824728 | MN823405 | MN823554 | |
JW 52011 | Garden soil | The Netherlands | MN824580 | MN824729 | MN823406 | MN823555 | |
JW 38012 | Garden soil | The Netherlands | MN824581 | MN824730 | MN823407 | MN823556 | |
JW 40007 | Garden soil | The Netherlands | MN824582 | MN824731 | MN823408 | MN823557 | |
JW 43007 | Garden soil | The Netherlands | MN824583 | MN824732 | MN823409 | MN823558 | |
Juxtiphoma eupyrena | JW 75002 | Garden soil | The Netherlands | MN824584 | MN824733 | MN823410 | MN823559 |
JW 116017 | Garden soil | The Netherlands | MN824585 | MN824734 | MN823411 | MN823560 | |
JW 170013 | Garden soil | The Netherlands | MN824586 | MN824735 | MN823412 | MN823561 | |
JW 79016 | Garden soil | The Netherlands | MN824587 | MN824736 | MN823413 | MN823562 | |
CBS 374.91; FMR 15329 | Solanum tuberosum | The Netherlands | LT623268 | FJ427110 | GU238072 | FJ426999 | |
JW 125024 | Garden soil | The Netherlands | MN824588 | MN824737 | MN823414 | MN823563 | |
JW 158014 | Garden soil | The Netherlands | MN824589 | MN824738 | MN823415 | MN823564 | |
JW 4010 | Garden soil | The Netherlands | MN824590 | MN824739 | MN823416 | MN823565 | |
JW 202020 | Garden soil | The Netherlands | MN824591 | MN824740 | MN823417 | MN823566 | |
J. kolkmaniorum | JW 125028 | Garden soil | The Netherlands | MN824592 | MN824741 | MN823418 | MN823567 |
CBS 146005T; JW 185006 | Garden soil | The Netherlands | MN824593 | MN824742 | MN823419 | MN823568 | |
JW 191004 | Garden soil | The Netherlands | MN824594 | MN824743 | MN823420 | MN823569 | |
JW 23021 | Garden soil | The Netherlands | MN824595 | MN824744 | MN823421 | MN823570 | |
JW 167004 | Garden soil | The Netherlands | MN824596 | MN824745 | MN823422 | MN823571 | |
JW 221010 | Garden soil | The Netherlands | MN824597 | MN824746 | MN823423 | MN823572 | |
JW 220011 | Garden soil | The Netherlands | MN824598 | MN824747 | MN823424 | MN823573 | |
JW 241011 | Garden soil | The Netherlands | MN824599 | MN824748 | MN823425 | MN823574 | |
JW 94009 | Garden soil | The Netherlands | MN824600 | MN824749 | MN823426 | MN823575 | |
CBS 527.66; FMR 15337 | Wheat field soil | Germany | LT623269 | FJ427111 | GU238073 | FJ427000 | |
JW 63001 | Garden soil | The Netherlands | MN824601 | MN824750 | MN823427 | MN823576 | |
JW 168007 | Garden soil | The Netherlands | MN824602 | MN824751 | MN823428 | MN823577 | |
Leptosphaeria doliolum | CBS 505.75T | Urtica dioica | The Netherlands | KT389640 | JF740144 | GQ387576 | JF740205 |
Leptosphaerulina australis | CBS 311.51 | Lawn | Switzerland | – | – | FJ795508 | – |
L. saccharicola | CBS 939.69 | Soil | The Netherlands | – | GU237541 | JX681098 | GU237911 |
L. trifolii | CBS 235.58 | Trifolium sp. | The Netherlands | – | GU237542 | GU237982 | GU237806 |
Macroventuria anomochaeta | CBS 525.71T | Decayed canvas | South Africa | GU456346 | GU237544 | GU237984 | GU237881 |
Ma. wentii | CBS 526.71T | Plant litter | USA | KT389642 | GU237546 | GU237986 | GU237884 |
Microsphaeropsis olivacea | CBS 233.77 | Pinus laricio | France | KT389643 | GU237549 | GU237988 | GU237803 |
CBS 442.83 | Taxus baccata | The Netherlands | – | GU237547 | EU754171 | GU237865 | |
Mi. proteae | CBS 111319T; CPC 1425 | Protea nitida | Unknown | – | JN712650 | JN712563 | JN712497 |
Neoascochyta argentina | CBS 112524T | Triticum aestivum | Argentina | – | KT389822 | KT389742 | KT389524 |
Neoa. desmazieri | CBS 297.69T | Lolium perenne | Germany | KT389644 | KT389806 | KT389726 | KT389508 |
Neoa. paspali | CBS 560.81T; PDDCC 6614 | Paspalum dilatatum | New Zealand | KP330426 | FJ427158 | GU238124 | FJ427048 |
Neoa. tardicrebrescens | CBS 689.97T | Hay | Norway | KT389654 | KT389824 | KT389744 | KT389526 |
Neoa. triticicola | CBS 544.74T | Triticum aestivum | South Africa | KT389652 | GU237488 | EU754134 | GU237887 |
Neodidymelliopsis cannabis | CBS 234.37 | Cannabis sativa | Unknown | KP330403 | GU237523 | GU237961 | GU237804 |
CBS 121.75T; IMI 194767; PD 73/584 | Urtica dioica | The Netherlands | – | GU237535 | GU237972 | GU237761 | |
Neod. polemonii | CBS 109181T; PD 83/757 | Polemonium caeruleum | The Netherlands | KP330427 | GU237648 | GU238133 | GU237746 |
Neod. xanthina | CBS 383.68T | Delphinium sp. | The Netherlands | KP330431 | GU237668 | GU238157 | GU237855 |
Neomicrosphaeropsis italica | MFLUCC 16-0284 | Tamarix sp. | Italy | KU714604 | – | KU900296 | KU900321 |
MFLUCC 15-0484 | Tamarix sp. | Italy | KU695539 | – | KU729853 | KU900319 | |
MFLUCC 15-0485T | Tamarix sp. | Italy | KU674820 | – | KU729854 | KU900318 | |
Nothophoma anigozanthi | CBS 381.91T; FMR 14914 | Anigozanthus maugleisii | The Netherlands | KT389655 | GU237580 | GU238039 | GU237852 |
N. arachidis-hypogaeae | CBS 125.93R; PD 77/1029 | Arachis hypogaea | India | KT389656 | GU237583 | GU238043 | GU237771 |
N. brennandiae | JW 1066 | Garden soil | The Netherlands | MN824603 | MN824752 | MN823429 | MN823578 |
CBS 145912T; JW 53011 | Garden soil | The Netherlands | MN824604 | MN824753 | MN823430 | MN823579 | |
MFLUCC 16-1392 | Ulmus (×) hollandica | Italy | KY053898 | KY053899 | KY053897 | KY053896 | |
N. gossypiicola | CBS 377.67; FMR 14912 | Gossypium sp. | USA | KT389658 | GU237611 | GU238079 | GU237845 |
UTHSC:DI16-294 | Human deep tissue/ fluids | USA | LT593082 | LT593012 | LN907437 | LT592943 | |
N. infossa | CBS 123395T | Fraxinus pennsylvanica | Argentina | KT389659 | FJ427135 | GU238089 | FJ427025 |
CBS 123394 | Fraxinus pennsylvanica | Argentina | – | FJ427134 | GU238088 | FJ427024 | |
N. macrospora | CBS 140674T; FMR 13767 | Human respiratory tract | USA | LT593073 | LN880539 | LN880537 | LN880536 |
N. pruni | MFLUCC 18-1600T | Prunus avium | China | MH853664 | MH853671 | MH827028 | MH827007 |
N. quercina | MFLUCC 18-1588 | Prunus avium | China | MH853665 | MH853672 | MH827029 | MH827008 |
CBS 633.92R; ATCC 36786 | Microsphaera alphitoides from Quercus sp. | Ukraine | KT389657 | GU237609 | EU754127 | GU237900 | |
UTHSC:DI16-270; FMR 13761 | Human superficial tissue | USA | LT593067 | LT592998 | LN907413 | LT592929 | |
N. variabilis | CBS 142457T; FMR 13777 | Human respiratory tract | USA | LT593078 | LT593008 | LN907428 | LT592939 |
Paraboeremia adianticola | CBS 260.92; PD 86/1103 | Pteris ensiformis | Unknown | – | KT389832 | KT389752 | KT389534 |
P. adianticola | CBS 187.83; PD 82/128; FMR 15344 | Polystichum adiantiforme | USA | KP330401 | GU237576 | GU238035 | GU237796 |
P. camelliae | CGMCC 3.18108 | Camellia sp. | China | KX829052 | KX829060 | KX829044 | KX829036 |
CGMCC 3.18106T | Camellia sp. | China | KX829050 | KX829058 | KX829042 | KX829034 | |
CGMCC 3.18107 | Camellia sp. | China | KX829051 | KX829059 | KX829043 | KX829035 | |
P. litseae | CGMCC 3.18110; LC 5030 | Litsea sp. | China | KX829046 | KX829054 | KX829038 | KX829030 |
JW 157001 | Garden soil | The Netherlands | MN824519 | MN824667 | MN823344 | MN823493 | |
CGMCC 3.18109T; LC 5028 | Litsea sp. | China | KX829045 | KX829053 | KX829037 | KX829029 | |
P. putaminum | JW 110005 | Garden soil | The Netherlands | MN824480 | MN824628 | MN823305 | MN823454 |
JW 126003 | Garden soil | The Netherlands | MN824481 | MN824629 | MN823306 | MN823455 | |
JW 265009 | Garden soil | The Netherlands | MN824482 | MN824630 | MN823307 | MN823456 | |
JW 221011 | Garden soil | The Netherlands | MN824483 | MN824631 | MN823308 | MN823457 | |
JW 165006 | Garden soil | The Netherlands | MN824484 | MN824632 | MN823309 | MN823458 | |
JW 232004 | Garden soil | The Netherlands | MN824485 | MN824633 | MN823310 | MN823459 | |
JW 192007 | Garden soil | The Netherlands | MN824486 | MN824634 | MN823311 | MN823460 | |
JW 125011 | Garden soil | The Netherlands | MN824487 | MN824635 | MN823312 | MN823461 | |
JW 18014 | Garden soil | The Netherlands | MN824488 | MN824636 | MN823313 | MN823462 | |
JW 142002 | Garden soil | The Netherlands | MN824489 | MN824637 | MN823314 | MN823463 | |
JW 221018 | Garden soil | The Netherlands | MN824490 | MN824638 | MN823315 | MN823464 | |
JW 238003 | Garden soil | The Netherlands | MN824491 | MN824639 | MN823316 | MN823465 | |
JW 192019 | Garden soil | The Netherlands | MN824492 | MN824640 | MN823317 | MN823466 | |
JW 213009 | Garden soil | The Netherlands | MN824493 | MN824641 | MN823318 | MN823467 | |
JW 226017 | Garden soil | The Netherlands | MN824494 | MN824642 | MN823319 | MN823468 | |
JW 109022 | Garden soil | The Netherlands | MN824495 | MN824643 | MN823320 | MN823469 | |
JW 4002 | Garden soil | The Netherlands | MN824496 | MN824644 | MN823321 | MN823470 | |
CBS 130.69R; IMI 331916 | Malus sylvestris | Denmark | – | GU237652 | GU238138 | GU237777 | |
JW 16015 | Garden soil | The Netherlands | MN824497 | MN824645 | MN823322 | MN823471 | |
JW 16001 | Garden soil | The Netherlands | MN824498 | MN824646 | MN823323 | MN823472 | |
JW 25002 | Garden soil | The Netherlands | MN824499 | MN824647 | MN823324 | MN823473 | |
JW 276009 | Garden soil | The Netherlands | MN824500 | MN824648 | MN823325 | MN823474 | |
JW 48011 | Garden soil | The Netherlands | MN824501 | MN824649 | MN823326 | MN823475 | |
JW 4011 | Garden soil | The Netherlands | MN824502 | MN824650 | MN823327 | MN823476 | |
JW 276008 | Garden soil | The Netherlands | MN824503 | MN824651 | MN823328 | MN823477 | |
JW 65008 | Garden soil | The Netherlands | MN824505 | MN824653 | MN823330 | MN823479 | |
JW 132016 | Garden soil | The Netherlands | MN824506 | MN824654 | MN823331 | MN823480 | |
JW 226014 | Garden soil | The Netherlands | MN824507 | MN824655 | MN823332 | MN823481 | |
JW 226015 | Garden soil | The Netherlands | MN824508 | MN824656 | MN823333 | MN823482 | |
JW 25012 | Garden soil | The Netherlands | MN824509 | MN824657 | MN823334 | MN823483 | |
P. putaminum | JW 11007 | Garden soil | The Netherlands | MN824510 | MN824658 | MN823335 | MN823484 |
JW 129005 | Garden soil | The Netherlands | MN824511 | MN824659 | MN823336 | MN823485 | |
CBS 372.91R; PD 75/690 | Ceratocystis ulmi | The Netherlands | – | GU237651 | GU238137 | GU237843 | |
JW 145026 | Garden soil | The Netherlands | MN824504 | MN824652 | MN823329 | MN823478 | |
JW 4006 | Garden soil | The Netherlands | MN824512 | MN824660 | MN823337 | MN823486 | |
JW 191017 | Garden soil | The Netherlands | MN824513 | MN824661 | MN823338 | MN823487 | |
JW 161002 | Garden soil | The Netherlands | MN824514 | MN824662 | MN823339 | MN823488 | |
JW 116031 | Garden soil | The Netherlands | MN824515 | MN824663 | MN823340 | MN823489 | |
JW 1008 | Garden soil | The Netherlands | MN824516 | MN824664 | MN823341 | MN823490 | |
JW 1020 | Garden soil | The Netherlands | MN824517 | MN824665 | MN823342 | MN823491 | |
JW 1046 | Garden soil | The Netherlands | MN824518 | MN824666 | MN823343 | MN823492 | |
P. rekkeri | JW 13016 | Garden soil | The Netherlands | MN824526 | MN824674 | MN823351 | MN823500 |
JW 13030 | Garden soil | The Netherlands | MN824527 | MN824675 | MN823352 | MN823501 | |
JW 79024 | Garden soil | The Netherlands | MN824528 | MN824676 | MN823353 | MN823502 | |
JW 25013 | Garden soil | The Netherlands | MN824529 | MN824677 | MN823354 | MN823503 | |
JW 167006 | Garden soil | The Netherlands | MN824530 | MN824678 | MN823355 | MN823504 | |
JW 132004 | Garden soil | The Netherlands | MN824531 | MN824679 | MN823356 | MN823505 | |
CBS 144949; JW 4024 | Garden soil | The Netherlands | MN824532 | MN824680 | MN823357 | MN823506 | |
JW 13017 | Garden soil | The Netherlands | MN824533 | MN824681 | MN823358 | MN823507 | |
JW 91008 | Garden soil | The Netherlands | MN824534 | MN824682 | MN823359 | MN823508 | |
JW 226002 | Garden soil | The Netherlands | MN824535 | MN824683 | MN823360 | MN823509 | |
JW 3018 | Garden soil | The Netherlands | MN824536 | MN824684 | MN823361 | MN823510 | |
CBS 144955T; JW 172002 | Garden soil | The Netherlands | MN824537 | MN824685 | MN823362 | MN823511 | |
JW 51014 | Garden soil | The Netherlands | MN824538 | MN824686 | MN823363 | MN823512 | |
JW 196020 | Garden soil | The Netherlands | MN824539 | MN824687 | MN823364 | MN823513 | |
CBS 144950; JW 6005 | Garden soil | The Netherlands | MN824540 | MN824688 | MN823365 | MN823514 | |
P. selaginellae | CBS 122.93T; PD 77/1049 | Selaginella sp. | The Netherlands | – | GU237656 | GU238142 | GU237762 |
P. truiniorum | JW 270002 | Garden soil | The Netherlands | MN824520 | MN824668 | MN823345 | MN823494 |
CBS 144952T; JW 47002 | Garden soil | The Netherlands | MN824521 | MN824669 | MN823346 | MN823495 | |
JW 147025 | Garden soil | The Netherlands | MN824522 | MN824670 | MN823347 | MN823496 | |
JW 182014 | Garden soil | The Netherlands | MN824523 | MN824671 | MN823348 | MN823497 | |
JW 192003 | Garden soil | The Netherlands | MN824524 | MN824672 | MN823349 | MN823498 | |
CBS 144961; JW 203021 | Garden soil | The Netherlands | MN824525 | MN824673 | MN823350 | MN823499 | |
Phoma herbarum | CBS 274.37 | Picea excelsa | UK | KT389662 | KT389835 | KT389754 | KT389537 |
CBS 615.75R; IMI 199779; PD 73/655 | Rosa multiflora cv. cathayensis | The Netherlands | KP330420 | FJ427133 | EU754186 | FJ427022 | |
Phomatodes aubrietiae | CBS 627.97T; PD 70/714 | Aubrietia sp. | The Netherlands | KT389665 | GU237585 | GU238045 | GU237895 |
Phomat. nebulosa | JW 166004 | Garden soil | The Netherlands | MN824609 | MN824758 | MN823435 | MN823584 |
JW 166006 | Garden soil | The Netherlands | MN824610 | MN824759 | MN823436 | MN823585 | |
JW 166013 | Garden soil | The Netherlands | MN824611 | MN824760 | MN823437 | MN823586 | |
CBS 100191 | Thlapsi arvense | Poland | KT389666 | KP330390 | KP330446 | KP330434 | |
CBS 117.93; PD 83/90 | Mercurialis perennis | The Netherlands | KP330425 | GU237633 | GU238114 | GU237757 | |
Pseudoascochyta novae-zelandiae | CBS 141689T; FMR 15110 | Cordyline australis | New Zealand | LT592895 | LT592894 | LT592893 | LT592892 |
Pse. pratensis | CBS 141688T; FMR 14524 | Soil | Spain | LT223133 | LT223132 | LT223131 | LT223130 |
Remotididymella anthropophylica | CBS 142462T; FMR 13770 | Human respiratory tract | USA | LT593075 | LT593005 | LN907421 | LT592936 |
R. destructiva | CBS 378.73T; FMR 15328 | Lycopersicon esculentum | Tonga | LT623258 | GU237601 | GU238063 | GU237849 |
Stagonosporopsis andigena | CBS 269.80; PD 75/914 | Solanum sp. | Peru | – | GU237675 | GU238170 | GU237817 |
S. astragali | CBS 178.25R; MUCL 9915 | Astragalus sp. | Unknown | – | GU237677 | GU238172 | GU237792 |
S. bomiensis | LC 8168 | Boraginaceae | China | KY742190 | KY742366 | KY742278 | KY742124 |
CGMCC 3.18366T; LC 8167 | Boraginaceae | China | KY742189 | KY742365 | KY742277 | KY742123 | |
S. crystalliniformis | CBS 713.85T; ATCC 76027; PD 83/826 | Lycopersicon esculentum | Colombia | KT389675 | GU237683 | GU238178 | GU237903 |
S. dorenboschii | CBS 426.90T; IMI 386093; PD 86/551 | Physostegia virginiana | The Netherlands | KT389678 | GU237690 | GU238185 | GU237862 |
S. hortensis | CBS 104.42R | – | The Netherlands | KT389680 | GU237703 | GU238198 | GU237730 |
CBS 572.85; PD 79/269 | Phaseolus vulgaris | The Netherlands | KT389681 | GU237704 | GU238199 | GU237893 | |
S. loticola | CBS 562.81T; PDDCC 6884 | Lotus pedunculatus | New Zealand | KT389684 | GU237697 | GU238192 | GU237890 |
S. papillata | LC 8170 | Rumex nepalensis | China | KY742192 | KY742368 | KY742280 | KY742126 |
CGMCC 3.18367T; LC 8169 | Rumex nepalensis | China | KY742191 | KY742367 | KY742279 | KY742125 | |
S. stuijvenbergii | CBS 144953T; JW 132011 | Garden soil | The Netherlands | MN824475 | MN824623 | MN823300 | MN823449 |
JW 33021 | Garden soil | The Netherlands | MN824476 | MN824624 | MN823301 | MN823450 | |
JW 14003 | Garden soil | The Netherlands | MN824477 | MN824625 | MN823302 | MN823451 | |
JW 44014 | Garden soil | The Netherlands | MN824478 | MN824626 | MN823303 | MN823452 | |
S. weymaniae | CBS 144959T; JW 201003 | Garden soil | The Netherlands | MN824479 | MN824627 | MN823304 | MN823453 |
Vacuiphoma bulgarica | CBS 357.84T | Trachystemon orientale | Bulgaria | LT623256 | GU237589 | GU238050 | GU237837 |
Vac. oculihominis | UTHSC:DI16-308T; FMR 13801 | Human superficial tissue | USA | LT593093 | LT593023 | LN907451 | LT592954 |
Vandijckomycella joseae | CBS 144948; JW 1068 | Garden soil | The Netherlands | MN824614 | MN824763 | MN823440 | MN823589 |
Van. joseae | CBS 143011T; JW 1073 | Garden soil | The Netherlands | MN824615 | MN824764 | MN823441 | MN823590 |
Van. snoekiae | CBS 144954T; JW 149017 | Garden soil | The Netherlands | MN824616 | MN824765 | MN823442 | MN823591 |
Xenodidymella applanata | CBS 115577 | Rubus idaeus | Sweden | KT389688 | KT389850 | KT389762 | KT389546 |
CBS 195.36T | Rubus idaeus | The Netherlands | – | KT389852 | KT389764 | KT389548 | |
CBS 205.63 | Rubus idaeus | The Netherlands | KP330402 | GU237556 | GU237998 | GU237798 | |
CBS 115578 | Rubus arcticus nothossp. stellarcticus | Sweden | – | KT389851 | KT389763 | KT389547 | |
X. asphodeli | CBS 375.62T | Asphodelus albus | France | KT389689 | KT389853 | KT389765 | KT389549 |
CBS 499.72 | Asphodelus ramosus | Italy | – | KT389853 | KT389766 | KT389550 | |
X. catariae | CBS 102635; PD 77/1131 | Nepeta catenaria | The Netherlands | KP330404 | GU237524 | GU237962 | GU237727 |
X. humicola | CBS 220.85R; PD 71/1030 | Franseria sp. | USA | KP330422 | GU237617 | GU238086 | GU237800 |
X. weymaniae | CBS 144960T; JW 201005 | Garden soil | The Netherlands | MN824613 | MN824762 | MN823439 | MN823588 |
A preliminary species identification of the strains was carried-out by a BLASTn search performed with each ITS and/or LSU sequence against the NCBI (http://blast.ncbi.nlm.nih.gov) and WI (http://www.westerdijkinstitute.nl/Collections) databases. The ITS and/or LSU sequences generated in this study with more than 98 % similarity with reference sequences for Didymellaceae were selected for further study (Table
To further study the phylogenetic relationships, reference sequences of Didymellaceae were downloaded from GenBank (Table
Bayesian analyses were performed using MrBayes v.3.2.6 (
Isolates of Didymellaceae were transferred to fresh oatmeal agar (OA), 2 % malt extract agar (MEA) and potato dextrose agar (PDA) (
A total of 293 soil samples were analysed, and nearly 3000 fungal strains were obtained. Among them, 148 Didymellaceae isolates were identified from 89 different garden soil samples, representing several locations in the Netherlands (Table
A multi-locus phylogeny comprising 325 strains, including the JW soil isolates and reference strains from GenBank, was used to infer the relationships among species in Didymellaceae (Figure
In the phylogenetic analysis, the 148 isolates from Dutch soil were distributed in 10 clades (Figure
Phylogenetic tree generated from the maximum-likelihood analysis based on the combined ITS, LSU, tub2 and rpb2 sequence alignment of Didymellaceae members. The RAxML bootstrap support values (BS), Bayesian posterior probabilities (PP), and parsimony bootstrap support values (PBS) are given at the nodes (BS/PP/PBS). BS and PBS values represent parsimony bootstrap support values >50 %. Full supported branches are indicated in bold. The scale bar represents the expected number of changes per site. Ex-type strains are represented in bold. Strains obtained in the current study are printed in green; among them, whilst strains that represent new taxa are printed in red. Some of the basal branches were shortened to facilitate layout (the fraction in round parentheses refers to the presented length compared to the actual length of the branch). The tree was rooted to Coniothyrium palmarum CBS 400.71 and Leptosphaeria doliolum CBS 505.75.
In the Juxtiphoma clade species clustered in two lineages, one corresponding to J. eupyrena (77/1/-) and the other representing a potentially new species (100/1/99). In the Paraboeremia clade, the soil isolates clustered in P. putaminum (86/0.99/67) and P. litseae (98/1/97). However, 21 isolates were distributed in two different lineages (with 6 and 15 isolates, respectively) that were phylogenetically distant from other species, representing two potentially new taxa. The soil isolates belonging to Stagonosporopsis clustered in a clade (100/1/99) that was phylogenetically distant from the other species, representing two potentially new species. In Didymella, the species were distributed in D. macrostoma (100/1/100) and D. pomorum (100/1/100), while isolates JW 195004 and JW 27006 were placed in two different branches, representing two putative new species. In Ascochyta one isolate grouped with A. syringae (93/1/86), whereas three isolates grouped in a different clade distant from previously known species, representing a potentially new species (100/1/100). The other three isolates grouped together at the bottom of the tree in a distant unknown lineage, which is introduced herein as a new genus with two species (100/1/90). All the new taxa are introduced in the taxonomy section based on the phylogenetic analysis and supported by morphological data. Descriptions and illustrations of the new taxa are provided in the taxonomy section below.
The single locus phylogenies of rpb2 and tub2 performed quite well at both generic and species levels. The rpb2 phylogeny was able to discriminate all 27 generic clades included in the phylogeny (Figure
benningiorum refers to Eva, Bas & Anne Benning who collected the soil sample from which the ex-type strain was isolated.
The Netherlands. Gelderland province, Wijchen, isolated from garden soil, Mar. 2017, E. Benning, B. Benning & A. Benning (holotype designated here CBS H-24104, living ex-type culture CBS 144957 = JW 196005).
Conidiomata pycnidial, mostly solitary, sometimes confluent, globose or subglobose, irregularly-shaped with age, brown to dark brown, glabrous, mostly produced on the agar surface and some immersed, 140–480(–580) × 100–370(–440) μm; with 1–6(–10) slightly papillate ostioles; pycnidial wall pseudoparenchymatous, 4–8 layers, 14.5–65 μm thick, outer layers composed of brown, flattened polygonal cells of 11–28 μm diam. Conidiogenous cells phialidic, hyaline, smooth, globose, ampulliform to lageniform, 5.5–9 × 4–6.5 μm. Conidia cylindrical, hyaline, smooth- and thin-walled, mostly straight, occasionally curved, aseptate, (3.5–)4.5–7 × 1.5–2.5 μm, 2-guttulate, small. Conidia matrix whitish.
Colonies after 7 d at 25 °C, on OA reaching 50–55 mm diam, aerial mycelium floccose, olivaceous to olivaceous black, buff towards the periphery, abundant production of pycnidia, margin irregular; reverse concolorous with the surface. On MEA reaching 40–45 mm diam, aerial mycelium floccose, concentric circles, centre pink, grey olivaceous, mouse grey, rosy buff toward periphery, moderate production of pycnidia, margin irregular; reverse orange, olivaceous black toward periphery. On PDA reaching 45–50 mm diam, aerial mycelium floccose, dark brick to olivaceous grey, buff towards periphery, abundant production of pycnidia, margin irregular; reverse concolorous with the surface. NaOH spot test negative on OA.
The Netherlands. Gelderland province, Wijchen, isolated from garden soil, Mar. 2017, E. Benning, B. Benning & A. Benning, JW 196023 = CBS 144958; ibid. JW 196013.
Ascochyta benningiorum is represented in the phylogenetic tree by three isolates (CBS 144957, CBS 144958 and JW 196013) from the same soil sample collected in Wijchen (Gelderland province). Ascochyta benningiorum grouped in a distinct clade close to A. phacae (Figure
Species in Ascochyta are commonly regarded as plant pathogens, especially of cereal crops and legumes (
Ascochyta benningiorum (CBS 144957). A, B Colony on OA (front and reverse) C, D colony on MEA (front and reverse) E, F colony on PDA (front and reverse) G pycnidia forming on OA H pycnidium I section of pycnidium J section of pycnidial wall K–M conidiogenous cells N conidia. Scale bars: 100 μm (H, I); 10 μm (J); 5 μm (K–N).
degraaffiae refers to Janne de Graaff who collected the soil sample from which the ex-type strain was isolated.
The Netherlands. Limburg province, Weert, isolated from garden soil, Mar. 2017, J. de Graaff (holotype designated here CBS H-24105, living ex-type culture CBS 144956 = JW 195004).
Conidiomata pycnidial, superficial on the agar or semi-immersed in the agar, scattered or aggregated, mostly confluent, globose, subglobose, lageniform to irregularly-shaped with age, brown to dark brown, ostiolate, covered by hyphal outgrowths, especially near the ostiole, 150–485 × 120–330 μm; non-papillate or with up to two papillate ostioles; pycnidial wall pseudoparenchymatous, 3–6 layers, 10–55 μm thick, outer layers composed of brown, isodiametric cells, 16–33 μm diam. Conidiogenous cells phialidic, hyaline, smooth, ampulliform, lageniform, pyriform or globose, 5.5–8.5 × 5–8 μm. Conidia ellipsoidal, oblong or oval, thin- and smooth-walled, hyaline, aseptate, 4.5–9(–11) × 3–4.5 μm, 2–6-guttulate, small. Conidial matrix milky white.
Colonies after 7 d at 25 °C, on OA reaching 65–70 mm diam, aerial mycelium floccose, orange to olivaceous, margin regular; reverse black near the centre, pale grey towards the periphery. On MEA reaching 55–60 mm diam, aerial mycelium floccose, buff to pale olivaceous, with white mycelium pellet and radially furrowed zones near the centre, margin regular; reverse buff near the centre, olivaceous to yellow towards the periphery. On PDA reaching 50–55 mm diam, aerial mycelium floccose, concentric circles pale brown, pale olivaceous grey, dark olivaceous, honey, margin irregular; reverse black with a pale olivaceous edge. NaOH spot test negative on OA.
In our phylogenetic analysis, D. degraaffiae grouped with D. americana and D. maydis (Figure
Didymella degraaffiae (CBS 144956). A, B Colony on OA (front and reverse) C, D colony on MEA (front and reverse) E, F colony on PDA (front and reverse) G, H pycnidia on OA I section of pycnidium J section of pycnidial wall K, L conidiogenous cells M chlamydospores N conidia. Scale bars: 50 μm (H, I); 10 μm (J); 5 μm (K–N).
kooimaniorum refers to Noud & Robin Kooiman who collected the soil sample from which the ex-type strain was isolated.
The Netherlands. Utrecht province, Vleuten, isolated from garden soil, Mar. 2017, N. Kooiman & R. Kooiman (holotype designated here CBS H-24106, living ex-type culture CBS 144951 = JW 27006).
Conidiomata pycnidial, superficial or semi-immersed, scattered or solitary, sometimes confluent, globose to subglobose, irregularly-shaped with age, pale brown to brown, covered by hyphal outgrowths, especially near the ostioles, 200–375 × 195–280 μm; with 1–3(–6) papillate ostioles; pycnidial wall pseudoparenchymatous, 3–5 layers, 10–35 μm thick, outer layers composed of pale brown, flattened polygonal cells of 16–32 μm diam. Conidiogenous cells phialidic, hyaline, smooth, ampulliform, lageniform or somewhat isodiametric, (4.5–)5.5–10 × 3.5–9 μm. Conidia ellipsoidal to oblong, straight, thin- and smooth-walled, hyaline, aseptate, 3.5–7 × 2–3 μm, 2-guttulate, big. Conidial matrix buff.
Colonies after 7 d at 25 °C, on OA reaching 55–60 mm diam, aerial mycelium floccose, pale smoke grey, pale brown towards periphery, abundant production of confluent pycnidia, margin regular; reverse pale olivaceous, with some olivaceous black zones. On MEA reaching 50–55 mm diam, aerial mycelium woolly, pale olivaceous grey, margin irregular; reverse buff near the centre, dark brown with orange edge. On PDA reaching 50–55 mm diam, aerial mycelium floccose, pale mouse grey with olivaceous edge, margin irregular; reverse dark brown with pale brown edge. NaOH spot test negative on OA.
Based on the multi-gene phylogenetic analyses, D. kooimaniorum forms an independent branch, clearly separated from other species in Didymella (Figure
Didymella kooimaniorum (CBS 144951). A, B Colony on OA (front and reverse) C, D colony on MEA (front and reverse) E, F colony on PDA (front and reverse) G pycnidia forming on OA H pycnidia I section of pycnidium J section of pycnidial wall K–M conidiogenous cells N conidia. Scale bars: 100 μm (H); 50 μm (I); 10 μm (J); 5 μm (K–N).
kolkmaniorum refers to Linde & Mette Kolkman who collected the soil sample from which the ex-type strain was isolated.
The Netherlands. Ophemert, isolated from garden soil, Mar. 2017, L. & M. Kolkman (holotype designated here CBS H-24214, living ex-type culture CBS 146005 = JW 185006).
Conidiomata pycnidial, superficial, solitary or confluent, globose to subglobose, brown to dark brown, glabrous, covered by dark hyphae and chlamydospores, 100–350 μm; uniostiolate papillate; pycnidial wall pseudoparenchymatous, 2–4 layers, 7.5–12.5 μm thick, outer layer composed of brown, flattened polygonal cells. Conidiogenous cells mono- or polyphialidic, hyaline, smooth, subcylindrical, ampulliform or somewhat isodiametric, 5.5–11.5 × 2.5–5.5 μm. Conidia ellipsoidal to oblong, straight or curved, thin- and smooth-walled, hyaline, aseptate, 3.5–7.5 × 2–3 μm, 1–3-guttulate, medium. Conidial matrix white to buff. Chlamydospores terminal or intercalary, solitary, or in simple or branched chains, barrel-shaped, subglobose or ellipsoidal, pale brown to brown, guttulate, 5.5–12 × 4–8 μm.
Colonies after 7 d at 25 °C, on OA reaching 45–60 mm diam, aerial mycelium cottony to floccose, isabelline to olivaceous, margin irregular; reverse concolorous. On MEA reaching 45–55 mm diam, aerial mycelium cottony to floccose, smoke grey to pale olivaceous grey with white edge, margin entire; reverse buff to smoke grey near the centre, olivaceous black with buff edge. On PDA reaching 45–50 mm diam, aerial mycelium cottony to floccose, olivaceous buff, dull green to buff, margin irregular; reverse smoke grey near the centre, olivaceous black with buff edge. NaOH spot test negative on OA.
Germany. Kiel-Kitzeberg, from wheat field soil, 1966, W. Gams, living cultures CBS 527.66 = FMR 15337 = ATCC 22238; The Netherlands. North Brabant province, Breda, isolated from garden soil, Mar. 2017, F. Versantvoort, JW 167004; ibid. JW 168007; Rijen, isolated from garden soil, Mar. 2017, G. & L. Schijvenaars, JW 94009. North Holland province, Hilversum, isolated from garden soil, Mar. 2017, S. Nieuwenhuijsen, JW 23021. Utrecht province, Amersfoort, isolated from garden soil, Mar. 2017, M. Kerssen, JW 125028; Amersfoort, isolated from garden soil, Mar. 2017, E., K. & O. de Jong Verpaalen, JW 241011; Amersfoort, isolated from garden soil, Mar. 2017, F. Wiegerinck, specimen CBS H-24102, culture CBS 145911 = JW 4017; Amersfoort, isolated from garden soil, Mar. 2017, T. & K. Wesselink, JW 191004; Bilthoven, isolated from garden soil, Mar. 2017, Y. El Ghazi, JW 220011; Utrecht, isolated from garden soil, Mar. 2017, J. Kooijmans, JW 63001.
Juxtiphoma kolkmaniorum is very similar and phylogenetically close to J. eupyrena. However, based on the multi-gene phylogenetic analyses, J. kolkmaniorum forms a separate clade (Figure
brennandiae refers to Kristel Brennand who collected the soil sample from which the ex-type strain was isolated.
The Netherlands. Limburg province, Ell, isolated from garden soil, Mar. 2017, K. Brennand (holotype designated here CBS H-24103, living ex-type culture CBS 145912 = JW 53011).
Conidiomata pycnidial, superficial to semi-immersed, solitary to confluent, globose to subglobose, irregularly-shaped with age, brown, setose, especially near the ostioles, 155–350 × 100–300 μm; with 1–4 papillate ostioles; pycnidial wall pseudoparenchymatous, 3–6 layers, 13.5–21.5 μm thick, outer layers composed of brown, flattened polygonal cells. Conidiogenous cells phialidic, hyaline, smooth, ampulliform or somewhat isodiametric, 3–5 × 5–8 μm. Conidia ellipsoidal, broadly ellipsoidal to oblong, straight, thick- and smooth-walled, hyaline becoming brown, aseptate, 3–8.5 × 1.5–3 μm, 1–6-guttulate, minute. Conidial matrix sepia to brown vinaceous.
Colonies after 7 d at 25 °C, on OA reaching 50–55 mm diam, aerial mycelium scarce, spore mass with grease-like appearance, dark brick to sepia, cinnamon to the edge, abundant production of confluent pycnidia, margin entire; reverse concentric rings umber to cinnamon. On MEA reaching 47–50 mm diam, aerial mycelium scarce, spore mass with grease-like appearance, dark brick to sepia, cinnamon to the edge, abundant production of confluent pycnidia, margin entire; reverse concentric rings umber to cinnamon. On PDA reaching 50–55 mm diam, aerial mycelium moderate to scarce, cottony, buff, spore mass with grease-like appearance, dark brick, ochreous to the edge, margin entire; reverse concentric rings dark brick to cinnamon. NaOH spot test negative on OA.
The Netherlands. North Holland province, Amsterdam, isolated from garden soil, Mar. 2017, J. van Dijk, JW 1066.
In the phylogenetic tree N. brennandiae was close to N. quercina and N. pruni (Figure
Nothophoma brennandiae (CBS 145912). A, B Colony on OA (front and reverse) C, D colony on MEA (front and reverse) E, F colony on PDA (front and reverse) G pycnidia forming on OA. H, I pycnidia J section of pycnidial wall K–M conidiogenous cells N conidia. Scale bars: 50 μm (H, I); 10 μm (J); 5 μm (K–N).
rekkeri refers to Daan Rekker who collected the soil sample from which the ex-type strain was isolated.
The Netherlands. Gelderland province, Geldermalsen, isolated from garden soil, Mar. 2017, D. Rekker (holotype designated here CBS H-24107, living ex-type culture CBS 144955 = JW 172002).
Conidiomata pycnidial, superficial, scattered or aggregated, solitary or confluent, globose or subglobose, irregularly-shaped with age, buff to brown, covered with abundant mycelial outgrowths especially when young, 150–390 × 120–320 μm; 1–2 papillate or non-papillate ostioles; pycnidial wall pseudoparenchymatous, 3–7 layers, 17.5–37 μm thick, outer layers composed of brown, flattened polygonal cells, 10–21 μm diam. Conidiogenous cells phialidic, hyaline, smooth, globose, subglobose or ampulliform, 5–10 × 4.5–7.5 μm. Conidia ellipsoidal to oblong, thin- and smooth-walled, hyaline, aseptate, 3.5–5 × 2.5–3 μm, with 2(–3) large guttules. Conidial matrix pink.
Colonies after 7 d at 25 °C, on OA reaching 75–80 mm diam, aerial mycelium floccose, saffron, vinaceous buff, pale olivaceous, margin regular; reverse concentric circles saffron, grey, olivaceous grey. On MEA reaching 55–60 mm diam, aerial mycelium floccose, margin irregular, pale olivaceous grey to whitish, orange near edge; reverse brown to dark brown, orange towards the periphery. On PDA reaching 70–75 mm diam, margin irregular, covered by felty aerial mycelium, buff, olivaceous grey towards periphery; reverse mouse, olivaceous towards periphery. NaOH spot test negative on OA.
Gelderland province, Culemborg, isolated from garden soil, Mar. 2017, H. van de Warenburg, JW 3018; Kapel-Avezaath, isolated from garden soil, Mar. 2017, A. Panneman, JW 79024; Meteren, isolated from garden soil, S. van Stuijvenberg, JW 132004; North Brabant province, Breda, isolated from garden soil, Mar. 2017, F. Wiegerinck, CBS 144949 = JW 4024; Breda, isolated from garden soil, Mar. 2017, F. Versantvoort, JW 167006; Zwanenburg, isolated from garden soil, Mar. 2017, J. Rebergen, JW 91008; North Holland province, Alkmaar, Mar. 2017, B. Verschoor, JW 13016, ibid. JW 13017 and JW13030; Utrecht province, Bilthoven, isolated from garden soil, Mar. 2017, H. Vos & S. Vos, JW 51014; Eemnes, isolated from garden soil, Mar. 2017, H.W. Vos, CBS 144950 = JW 6005; Hooglanderveen, isolated from garden soil, Mar. 2017, F. Rijpma, JW 25013; Utrecht, isolated from garden soil, R. van Zijl, JW 226002.
Paraboeremia rekkeri formed a well-supported (1.0/100/96) distinct lineage in Paraboeremia (Figure
Paraboeremia rekkeri (CBS 144955). A, B Colony on OA (front and reverse) C, D colony on MEA (front and reverse) E, F colony on PDA (front and reverse) G pycnidia forming on OA H pycnidium I section of pycnidium J section of pycnidial wall K–N conidiogenous cells O conidia. Scale bars: 100 μm (H); 20 μm (I); 10 μm (J); 5 μm (K–O).
truiniorum refers to Cuno & Tygo Truin who collected the soil sample from which the ex-type strain was isolated.
The Netherlands. Gelderland province, Barneveld, Voorthuizen, isolated from garden soil, Mar. 2017, C. Truin & T. Truin (holotype designated here CBS H-24108, living ex-type culture CBS 144952 = JW 47002).
Conidiomata pycnidial, superficial, scattered or aggregated, most solitary, globose or subglobose, confluent and irregularly-shaped with age, pale brown, thick-walled, covered with abundant mycelial outgrowths, 160–420 × 135–430 μm; 1-papillate or non-papillate ostioles, sometimes elongated to a short neck; pycnidial wall pseudoparenchymatous, 7–11 layers, 40–70 μm thick, outer layers composed of brown, flattened polygonal cells of 22–45.5 μm diam. Conidiogenous cells phialidic, hyaline, smooth, globose, subglobose, ampulliform or doliiform, 4.5–8.5 × 4–7 μm. Conidia ellipsoidal to oblong, thin- and smooth-walled, hyaline, aseptate, 3.5–5 × 2–3 μm, with (1–)2 large guttules. Conidial matrix whitish.
Colonies after 7 d at 25 °C, on OA reaching 70–75 mm diam, aerial mycelium floccose, vinaceous buff to hazel, margin regular; reverse buff to olivaceous. On MEA reaching 65–70 mm diam, aerial mycelium felty, whitish, pale mouse grey toward periphery, margin regular; reverse dark brick to dark brown, with pale brown edge. On PDA reaching 75–80 mm diam, aerial mycelium felty, olivaceous buff to pale mouse grey, olivaceous toward periphery, margin irregular; reverse mouse grey, olivaceous toward periphery. NaOH spot test negative on OA.
The Netherlands, Gelderland province, Culemborg, isolated from garden soil, Mar. 2017, R. Fuld, JW 182014; The Netherlands. South Holland province, Alphen aan den Rijn, isolated from garden soil, Mar. 2017, K. Boutwell, CBS 144961 = JW 203021; The Netherlands. South Holland province, Gorinchem, isolated from garden soil, Mar. 2017, L. van Rosmalen, JW 270002; The Netherlands. Utrecht province, Utrecht, isolated from garden soil, Mar. 2017, L. van Rijnberk, JW 147025; The Netherlands. Utrecht province, Woerden, isolated from garden soil, Mar. 2017, L. Borsboom, JW 192003.
Based on the phylogenetic analyses, P. truiniorum is represented by six isolates, forming a distinct lineage (Figure
Paraboeremia truiniorum (CBS 144952). A, B Colony on OA (front and reverse) C, D colony on MEA (front and reverse) E, F colony on PDA (front and reverse) G pycnidia forming on OA H pycnidium I section of pycnidium J section of pycnidial wall K–N conidiogenous cells O conidia. Scale bars: 20 μm (H); 50 μm (I); 5 μm (J–O).
stuijvenbergii refers to Simon van Stuijvenberg, who collected the soil sample from which the ex-type strain was isolated.
The Netherlands. Gelderland province, Meteren, from garden soil, Mar. 2017, S. van Stuijvenberg (holotype designated here CBS H-24109; living ex-type culture CBS 144953 = JW 132011).
Conidiomata pycnidial, produced on the agar surface, scattered or aggregated, solitary globose to subglobose, or 4–7(–10) confluent and irregularly-shaped, brownish, glabrous, ostiolate, 200–1000 × 195–930 μm; with 1–2 slightly papillate ostioles, sometimes elongated to a short neck; pycnidial wall pseudoparenchymatous, 4–5 layers, 6.5–35 μm thick, outer layers composed of brown, flattened polygonal cells, 9.5–33 μm diam. Conidiogenous cells phialidic, hyaline, smooth, globose, ampulliform or lageniform, 4.5–9 × 4–8 μm. Conidia ellipsoidal to oblong, smooth- and thin-walled, hyaline, aseptate, 3.5–6.5 × 2–3 μm, 1–2-guttulate. Conidial matrix whitish.
Colonies after 7 d at 25 °C, on OA reaching 75–80 mm diam, floccose aerial mycelium, olivaceous to pale olivaceous, whitish to pink near the edge, margin regular; reverse iron grey. On MEA reaching 65–70 mm diam, margin regular, aerial mycelium floccose, vinaceous buff with olivaceous edge; reverse darker brown with olivaceous black edge, buff near the centre. On PDA reaching 70–75 mm diam, margin regular, covered by floccose aerial mycelium, olivaceous, olivaceous black towards periphery, with pinkish to pale brown edge; reverse iron-grey, buff towards periphery. NaOH spot test negative on OA.
The Netherlands, Gelderland province, Arnhem, from garden soil, Mar. 2017, D. Peters, JW 14003; Utrecht province, Utrecht, from garden soil, Mar. 2017, N. Francisca, JW 44014; Utrecht, from garden soil, Mar. 2017, P. de Koff, JW 33021.
Phylogenetically, S. stuijvenbergii is most closely related to S. weymaniae, another novel species collected from Dutch soil in this study (Figure
Stagonosporopsis stuijvenbergii (CBS 144953). A, B Colony on OA (front and reverse) C, D colony on MEA (front and reverse) E, F colony on PDA (front and reverse) G pycnidia forming on OA H pycnidia I ostiole J–L conidiogenous cells M stromatic hyphal aggregations N conidia. Scale bars: 50 μm (H); 10 μm (I, M); 5 μm (J–L, N).
weymaniae refers to Anna Weyman, who collected the soil sample from which the ex-type strain was isolated.
The Netherlands. Utrecht province, Baarn, isolated from garden soil, Mar. 2017, A. Weyman (holotype designated here CBS H-24110; living ex-type culture CBS 144959 = JW 201003).
Conidiomata pycnidial, semi-immersed or immersed, mostly solitary, scattered or aggregated, (sub-)globose, whitish to buff, glabrous, 330–650 × 250–550 μm; non-ostiolate or with a single, inconspicuous ostiole; pycnidial wall pseudoparenchymatous, 2–9 layers, 20–60 μm thick, outer layers composed of hyaline, flattened polygonal cells. Conidiogenous cells phialidic, hyaline, smooth, (sub-)globose to ampulliform, 4.5–7.5 × 4–7.5 μm. Macroconidia oblong, smooth- and thin-walled, hyaline, aseptate, 4–6.5(–8) × 2–3 μm, 1–3(–4)-guttulate, with one large central guttule or two large polar guttules. Microconidia produced in the same pycnidia with macroconidia, globose to subglobose, smooth, hyaline, aseptate, 3–4 × 2.5–3.5 μm, with a single, small guttule. Conidial matrix whitish. Chlamydospores unicellular, intercalary in chains, barrel-shaped, thick-walled, pale brown to green brown, guttulate, 9.5–14 × 11–16 μm diam.
Colonies after 7 d at 25 °C, on OA reaching 70–75 mm diam, sparse aerial mycelium, buff to pale olivaceous with sparse olivaceous zones, darker grey near the centre, abundant production of buff pycnidia, margin regular; reverse pale olivaceous, olivaceous black near the centre. On MEA reaching 80–85 mm diam, margin regular, aerial mycelium floccose, yellow to vinaceous buff; reverse orange to olivaceous. On PDA reaching 75–80 mm diam, margin regular, covered by floccose aerial mycelium, centre vinaceous buff, dark olivaceous towards the periphery with production of buff pycnidia; reverse olivaceous black, olivaceous towards the periphery. NaOH spot test: pale reddish discolouration on OA plate.
Stagonosporopsis weymaniae is phylogenetically closely related to S. stuijvenbergii (Figure
Stagonosporopsis weymaniae (CBS 144959). A, B Colony on OA (front and reverse) C, D colony on MEA (front and reverse) E, F colony on PDA (front and reverse) G–I pycnidia forming on OA J, L conidiogenous cells K subglobose conidia M stromatic hyphal aggregations N chlamydospores O oblong conidia. Scale bars: 100 μm (I); 10 μm (J–N); 5 μm (O).
Named in honour of José F.T.M. van Dijck, who was elected as the first female President (2015–2018) of the Royal Dutch Academy of Arts and Sciences (KNAW).
Vandijckomycella joseae Hern.-Restr., L.W. Hou, L. Cai & Crous.
Conidiomata pycnidial, superficial on the surface of the agar, solitary or confluent, globose to lageniform, covered by hyphal outgrowths, ostiolate, pycnidial wall pseudoparenchymatous, with 3–9 layers. Conidiogenous cells phialidic, hyaline, smooth, globose or ampulliform. Conidia hyaline, smooth- and thin-walled, aseptate, ovoid, oblong or ellipsoidal, with 2–4 polar guttules.
Named in honour of the first female President (2015–2018) of the Royal Dutch Academy of Arts and Sciences (KNAW), José F.T.M. van Dijck, who collected the soil sample from which the ex-type strain was isolated.
The Netherlands. North Holland province, Amsterdam, isolated from garden soil, Mar. 2017, J.F.T.M. van Dijk (holotype designated here CBS H-24112; living ex-type culture CBS 143011 = JW 1073).
Conidiomata pycnidial, produced on the agar surface, scattered or aggregated, solitary, (sub-)globose, confluent and irregularly-shaped with age, pale brown, covered in abundant long and thin mycelium hair, 150–340 × 130–250 μm; with 1–2 slightly papillate or non-papillate ostioles, sometimes elongated to a short neck; pycnidial wall pseudoparenchymatous, 3–5 layers, 13–25 μm thick, outer layers composed of brown, flattened, polygonal cells of 10–23 μm diam. Conidiogenous cells phialidic, hyaline, smooth, globose, ampulliform, lageniform or subglobose, 5–8(–9.5) × 4–8 μm. Conidia ellipsoidal to oblong, smooth- and thin-walled, hyaline, aseptate, 3.5–5.5 × 2–2.5 μm, (1–)2(–3)-guttulate. Conidial matrix whitish.
Colonies after 7 d at 25 °C, on OA reaching 75–80 mm diam after 7 d, covered by woolly aerial mycelium, concentric circles, pale olivaceous grey, pink, pale greenish grey, whitish near the edge, margin regular; reverse concentric circles dark brown, pale brown, orange, and pale olivaceous. On MEA reaching 75–80 mm diam, aerial mycelium woolly, margin regular, pale olivaceous grey; reverse dark brown, reddish towards the periphery. On PDA reaching 75–80 mm diam, margin regular, covered by felty aerial mycelium, pale olivaceous grey or olivaceous grey, with whitish parts near the centre or through the plate; reverse zonate, orange to reddish, brown and yellow. NaOH spot test: a coral discolouration on OA.
The Netherlands. North Holland province, Amsterdam, isolated from garden soil, Mar. 2017, J.F.T.M. van Dijk, CBS 144948 = JW 1068.
The new genus Vandijckomycella is introduced to accommodate two new species isolated from soil samples which form an independent lineage in Didymellaceae, being clearly separated from other genera (Figure
Vandijckomycella joseae (CBS 143011). A, B Colony on OA (front and reverse) C, D colony on MEA (front and reverse) E, F colony on PDA (front and reverse) G, H pycnidia forming on OA I, J section of pycnidial wall K–N conidiogenous cells O conidia. Scale bars: 100 μm (H); 20 μm (I); 10 μm (J); 5 μm (K–O).
snoekiae refers to Rana Marit Ida Snoek who collected the soil sample from which the ex-type strain was isolated.
The Netherlands. Utrecht province, Utrecht, isolated from garden soil, Mar. 2017, R.M.I. Snoek (holotype designated here CBS H-24111, living ex-type culture CBS 144954 = JW 149017).
Conidiomata pycnidial, superficial on the agar or covered under a thick mycelial layer, scattered or aggregated, mostly solitary, globose to subglobose, sometimes confluent, ellipsoidal, dark brown, covered by abundant long hyphal outgrowths, 150–650(–850) × 145–600(–730) μm; ostioles inconspicuous; pycnidial wall pseudoparenchymatous, 5–9 layers, 37–58.5 μm thick, outer layers composed of brown, flattened polygonal cells, 10–23 μm diam. Conidiogenous cells phialidic, hyaline, smooth, globose, ampulliform or lageniform, 5–8.5 × 5–7.5 μm. Conidia oblong, smooth- and thin-walled, hyaline, aseptate, 4–6.5 × 2–2.5 μm, with two small polar guttules. Conidial matrix whitish.
Colonies after 7 d at 25 °C, on OA reaching 50–55 mm diam after 7 d, covered by floccose aerial mycelium, pink to grey, darker grey near the centre, margin regular; reverse black near the centre, yellow towards the periphery. On MEA reaching 50–55 mm diam, aerial mycelium floccose to cottony, buff with some mouse grey zones, margin regular; reverse orange with some radial yellow lines and some black zones. On PDA, reaching 45–50 mm diam, covered by floccose aerial mycelium, vinaceous grey to pale olivaceous, olivaceous grey near the centre, margin irregular; reverse buff to orange, black near the centre. NaOH spot test on OA: pale reddish discolouration.
Morphologically, V. snoekiae differs from its closest phylogenetic neighbour V. joseae in the size of its pycnidia and the number of ostioles. Vandijckomycella snoekiae produces larger pycnidia with inconspicuous ostioles, measuring 150–650(–850) × 145–600(–730) μm, while V. joseae produces pycnidia with 1–2 ostioles, measuring 150–340 × 130–250 μm. In addition, V. snoekiae produces conidia with less and smaller guttules than V. joseae (2 guttules, vs. 1–3 large guttules).
Vandijckomycella snoekiae (CBS 144954). A, B Colony on OA (front and reverse) C, D colony on MEA (front and reverse) E, F colony on PDA (front and reverse) G, H pycnidia forming on OA I, J section of pycnidial wall K–N conidiogenous cells O conidia. Scale bars: 100 μm (H); 50 μm (I); 10 μm (J); 5 μm (K–O).
weymaniae refers to Anna Weyman who collected the soil sample from which the ex-type strain was isolated.
The Netherlands. Utrecht province, Baarn, isolated from garden soil, Mar. 2017, A. Weyman (holotype designated here CBS H-24113; living ex-type culture CBS 144960 = JW 201005).
Conidiomata pycnidial, semi-immersed on the agar, mostly confluent, sometimes solitary, scattered or aggregated, subglobose or ellipsoidal, irregularly-shaped when confluent, dark brown, ostiolate, glabrous or with long hyphal outgrowths around the ostiole, 100–700 × 100–400(–590) μm; with 1–2(–6) ostioles, papillate or elongated into a long neck, up to 113 μm in length; pycnidial wall pseudoparenchymatous, 3–5 layers, 17–45 μm thick, outer layers composed of pale brown to brown, flattened polygonal cells of 10–35 μm diam. Conidiogenous cells phialidic, hyaline, smooth, sub-globose, ampulliform or lageniform, 4.5–8 × 4–6.5 μm. Conidia oblong, smooth- and thin-walled, hyaline, aseptate, 4–6(–8) × 2–2.5 μm, with two small, polar guttules. Conidial matrix whitish.
Colonies after 7 d at 25 °C, on OA reaching 55–60 mm diam, aerial mycelium floccose near the centre, flat towards the periphery, pale olivaceous to whitish, black pycnidia visible near the centre, margin regular; reverse buff to salmon, pale olivaceous towards the periphery. On MEA reaching 40–45 mm diam, aerial mycelium felty, sectors with cottony mycelium, white, buff to pale olivaceous, margin regular; reverse yellow to orange, dark brown and pale grey near the centre. On PDA reaching 45–60 mm, aerial mycelium floccose, whitish in the centre, honey towards the periphery, margin regular; reverse concentric circles dark brown in centre, orange, yellow, buff towards the periphery. NaOH spot test negative on OA.
Xenodidymella weymaniae formed a distinct branch basal to X. applanata (Figure
Xenodidymella weymaniae (CBS 144960). A, B Colony on OA (front and reverse) C, D colony on MEA (front and reverse) E, F colony on PDA (front and reverse) G, H pycnidia forming on OA I, J section of pycnidial wall K–N conidiogenous cells O conidia. Scale bars: 50 μm (H); 20 μm (I); 10 μm (J); 5 μm (K–O).
During the present Citizen Science project which focused on Dutch soil fungi, numerous unknown species of filamentous and yeast fungi were described (
As one of the largest families in the fungal kingdom, at least 26 genera are accepted in Didymellaceae (
Paraboeremia and Juxtiphoma were the most dominant genera. Species of Paraboeremia are more common on plants than in soil, except for P. putaminum, which is regarded as a widespread soil-borne fungus isolated from the subterranean parts of various herbaceous and woody plants (
The second most abundant species was Juxtiphoma eupyrena. The monotypic genus Juxtiphoma was recently introduced to accommodate Phoma eupyrena (
Among our isolates we found Phomatodes nebulosa, Didymella macrostoma and D. pomorum which are plurivorous and cosmopolitan species often isolated from soil (
These findings suggest that species of Didymellaceae are also widely distributed in soil. Previous studies have revealed that many pathogens survive in soil by producing resting bodies (
Recently, additional research based on cultivation-independent and cultivation-dependent methods has revealed that Didymellaceae species present in various soil environments are more diverse than one might have expected (
In summary, results of our study revealed the presence of a large number of unknown species and even a novel genus in soil, illustrating that this substrate is an important source for the discovery of novel taxa, and demonstrating that species diversity of Didymellaceae in soil is considerably greater than current estimates.
This study was financially supported by the Utrecht University Museum and the Royal Dutch Academy of Arts and Sciences for promoting the Citizen Science project, and for providing a platform to facilitate interaction with various Dutch primary schools. Lingwei Hou acknowledges CAS QYZDB-SSW-SMC044 for supporting her postgraduate studentship.
We are grateful to all the children and parents who participated in this project, collecting samples in their gardens and submitting them to the Westerdijk Institute for analyses; to José F.T.M. van Dijck, the first female President (2015–2018) of the Royal Dutch Academy of Arts and Sciences, who enthusiastically took part in this project and submitted the first soil sample in the Citizen Science Project. We are thankful to the staff from the Westerdijk Institute: Manon Verweij, Karin Schagen and Mariëtte Oosterwegel for promoting the project and establishing communication with the collectors and schools; to Trix Merkx and Arien van Iperen for depositing the isolates and specimens in the culture collection and fungarium.