Comparison of Culturing and Metabarcoding Methods to Describe the Fungal Endophytic Assemblage of Brachypodium rupestre Growing in a Range of Anthropized Disturbance Regimes
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. The Study Area
2.2. Plant Sampling
2.3. Isolation and Identification of Fungi Using the Culturing Method
2.4. Metabarcoding Analysis and Taxonomic Assignment
2.5. Data Analysis
3. Results
3.1. Comparison of B. rupestre Mycobiome Obtained by Culturing and Metabarcoding Methods
3.2. The Mycobiome of B. rupestre According to the Metabarcoding Method
3.2.1. Fungal Endophytic Richness and Diversity
3.2.2. Taxonomic Assemblages for Grassland Types and Tissues
3.2.3. Indicator Species of the Fungal Assemblages
4. Discussion
4.1. The Mycobiome of B. rupestre According to the Metabarcoding Data
4.2. Culturing vs. Metabarcoding Methods
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Appendix A
Match Taxon (NCBI) | Match Taxon (UNITE) | |||||||
---|---|---|---|---|---|---|---|---|
Accession Number | Greatest Percentage Identity (%) | Accession Number | Greatest Percentage Identity (%) | Taxon Proposed | Accession Number | |||
1 | Gerronema sp. | NR_166278 | 82.37 | Delicatula integrella | UDB034203 | 99.77 | Agaricales A | OK430888 |
2 | Gerronema sp. | NR_166278 | 78.9 | Mycena sp. | KT224934 | 89 | Agaricales B | OK430889 |
3 | Ramariopsis flavescens | NR_119913 | 85.06 | Agaricales | JX456916 | 95.2 | Agaricales C | OK430890 |
4 | Gerronema indigoticum | NR_166278 | 78.06 | Mycenaceae | KT224934 | 94.29 | Agaricales D | OK430891 |
5 | Laccaria aurantia | NR_154113 | 78.57 | Mycena floridula | MH856660 | 99.35 | Agaricales E | OK430892 |
6 | Radulotubus resupinatus | NR_153458 | 84.66 | Agaricomycetes | LR864837 | 99.32 | Agaricomycetes | OK430893 |
7 | Lachnellula hyalina | NR_165202 | 93.02 | Albotricha sp. | JN995639 | 100 | Albotricha sp. A | OK430894 |
8 | Lachnellula hyalina | NR_165202 | 91.59 | Albotricha sp. | JN995639 | 98.71 | Albotricha sp. B | OK430895 |
9 | Lachnellula hyalina | NR_165202 | 91.59 | Albotricha sp. | HM136666 | 100 | Albotricha sp. C | OK430896 |
10 | Funiliomyces biseptatus | NR_159862 | 96.39 | Acremonium sp. | MT911439 | 100 | Ascomycota A | OK430897 |
11 | Tricladium terrestre | NR_160144 | 93.67 | Ascomycota sp. | KR266584 | 93.67 | Ascomycota B | OK430898 |
12 | Auricularia scissa | NR_125807 | 80.48 | Oliveonia sp. | MT235652 | 97.16 | Auriculariales | OK430899 |
13 | Hydnum albidum | NR_164025 | 78.7 | Sistotrema sp. | KC965692 | 93.87 | Cantharellales | OK430900 |
14 | Codinaeae sp. | NR_168799 | 97.52 | Codinaea sp. | MT626587 | 98.35 | Chaetosphaeriaceae | OK430901 |
15 | Chalara hyalocuspica | NR_137568 | 91.25 | Chalara sp. | MK965778 | 98.33 | Chalara sp. | OK430902 |
16 | Cladophialophora tengchongensis | NR_172399 | 90.07 | Cladophialophora sp. | KP889848 | 100 | Cladophialophora sp. | OK430903 |
17 | Coccomyces pinicola | NR_158295 | 83.54 | Coccomyces dentatus | KU986782 | 93.82 | Coccomyces sp. | OK430904 |
18 | Conlarium duplumascospora | NR_138382 | 94.9 | Conlarium sp. | MK164654 | 96.85 | Conlarium sp. | OK430905 |
19 | Laburnicola centaurear | NR_154131 | 93.6 | Laburnicola sp. | MK018553 | 97.95 | Didymosphaeriaceae | OK430906 |
20 | Pseudoseptoria collariana | NR_156560 | 97.63 | Pseudoseptoria donacis | MH859141 | 99.6 | Dothideales | OK430907 |
21 | Roussoella thailandica | NR_155717 | 80.56 | Dothideomycetes | KJ827952 | 95 | Dothideomycetes A | OK430908 |
22 | Pirozynskiella laurisilvica | NR_153488 | 91 | Capnodiales | KX403688 | 91 | Dothideomycetes B | OK430909 |
23 | Drechslera sp. | NR_164466 | 92.89 | Drechslera sp. | MT816433 | 99.6 | Drechslera sp. | OK430910 |
24 | Entoloma luteofuscum | NR_152900 | 95.24 | Entoloma conferendum | MT741744 | 100 | Entoloma sp. | OK430911 |
25 | Epicoccum phragmospora | NR_165920 | 99.19 | Epicoccum sp. | MW054426 | 100 | Epicoccum sp. | OK430912 |
26 | Falciphora oryzae | NR_153972 | 98.86 | Falciphora oryzae | MH201898 | 99.23 | Falciphora sp. | OK430913 |
27 | Glarea lozoyensis | NR_137138 | 98.48 | Glarea sp. | KT268823 | 100 | Glarea sp. | OK430914 |
28 | Glarea lozoyensis | NR_137138 | 95.96 | Glarea sp. | KF617491 | 100 | Helotiaceae | OK430915 |
29 | Loramyces macrosporus | NR_138379 | 89.8 | Loramyces sp. | KF618060 | 99.58 | Helotiales A | OK430916 |
30 | Loramyces macrosporus | NR_138379 | 89.07 | Mollisia sp. | UDB0778890 | 99.59 | Helotiales B | OK430917 |
31 | Triposporium cycadicola | NR_156587 | 89.71 | Hymenoscyphus sp. | HQ625461 | 99.58 | Helotiales C | OK430918 |
32 | Bisporella shangrilana | NR_153628 | 97.02 | Helotiales | LR863043 | 99.58 | Helotiales D | OK430919 |
33 | Hyaloscypha finlandica | NR_121279 | 92.27 | Hyaloscypha vraolstadiae | KC876248 | 96.23 | Hyaloscyphaceae | OK430920 |
34 | Lachnellula hyalina | NR_165202 | 91.12 | Lachnum sp. | MT913626 | 96.61 | Lachnum sp. A | OK430921 |
35 | Lachnum fusiforme | NR_154122 | 89.91 | Lachnum sp. | MK808968 | 97.45 | Lachnum sp. B | OK430922 |
36 | Proliferodiscus sp. | NR_164304 | 86.67 | Lachnum sp. | MH628228 | 99.57 | Lachnum sp. C | OK430923 |
37 | Leohumicola minima | NR_121307 | 100 | Leohumicola sp. | FM999596 | 100 | Leohumicola sp. | OK430924 |
38 | Variabilispora flava | NR_165906 | 86.83 | Helotiales | AY969994 | 95.65 | Leotiomycetes | OK430925 |
39 | Menispora ciliata | NR_171740 | 99.5 | Menispora ciliata | MH860017 | 99.12 | Menispora sp. | OK430926 |
40 | Microdochium phragmitis | NR_132916 | 100 | Microdochium phragmitis | MN077456 | 100 | Microdochium sp. | OK430927 |
41 | Phialocephala sp. | NR_119482 | 90.38 | Phialocephala sp. | MG066460 | 97.88 | Mollisiaceae A | OK430928 |
42 | Mollisia scopiformis | NR_119460 | 93.22 | Phialocephala sp. | MK808244 | 98.72 | Mollisiaceae B | OK430929 |
43 | Mollisia monilioides | NR_171261 | 96.22 | Phialocephala sp. | MT911435 | 100 | Mollisiaceae C | OK430930 |
44 | Mollisia prismatica | NR_171258 | 91.9 | Phialocephala sp. | MK965789 | 99.57 | Mollisiaceae D | OK430931 |
45 | Mollisia asteliae | NR_173037 | 95.15 | Mollisia sp. | MH633925 | 100 | Mollisiaceae E | OK430932 |
46 | Mollisia diesbachiana | NR_171259 | 96.77 | Mollisia sp. | MT179560 | 100 | Mollisiaceae F | OK430933 |
47 | Mortierella gemmifera | NR_111559 | 94.81 | Mortierellaceae | LR863033 | 99.43 | Mortierella sp. | OK430934 |
48 | Podila horticola | NR_111572 | 99.09 | Mortierella sp. | DQ388818 | 99.7 | Mortierellaceae | OK430935 |
49 | Mycena fulgoris | NR_163300 | 93.29 | Mycena sp. | JF519186 | 98.4 | Mycena sp. A | OK430936 |
50 | Mycena fulgoris | NR_163300 | 93.29 | Mycena sp. | MK961197 | 99.67 | Mycena sp. B | OK430937 |
51 | Mycena fulgoris | NR_163300 | 93.31 | Mycena arcangeliana | JF908402 | 99.35 | Mycena sp. C | OK430938 |
52 | Mycena fulgoris | NR_163300 | 87.99 | Mycena sp. | UDB020406 | 100 | Mycena sp. D | OK430939 |
53 | Mycena fulgoris | NR_163300 | 89.64 | Mycena sp. | HQ625481 | 99.32 | Mycena sp. E | OK430940 |
54 | Cercospora coniogrammes | NR_147260 | 97.89 | Cercospora sp. | MN970528 | 97.89 | Mycosphaerellaceae | OK430941 |
55 | Myrmecridium spartii | NR_155376 | 96.25 | Myrmecridium sp. | MW133876 | 98.32 | Myrmecridium sp. | OK430942 |
56 | Pseudomassariella vexata | NR_164217 | 87.78 | Fusidium sp. | HG936132 | 100 | Nectriaceae | OK430943 |
57 | Neoascochyta europaea | NR_136131 | 97.03 | Neoascochyta europaea | MK190674 | 97.17 | Neoascochyta sp. A | OK430944 |
58 | Neoascochyta soli | NR_158269 | 100 | Neoascochyta paspali | MT373264 | 100 | Neoascochyta sp. B | OK430945 |
59 | Ophiosphaerella aquatica | NR_154352 | 89.96 | Ophiosphaerella sp. | MH063799 | 98.38 | Ophiosphaerella sp. | OK430946 |
60 | Paracamarosporium fagi | NR_154318 | 99.18 | Paracamarosporium fagi | MN244221 | 99.18 | Paracamarosporium sp. | OK430947 |
61 | Parasola parvula | NR_160509 | 94.43 | Parasola schroeteri | UDB024639 | 99.67 | Parasola sp. | OK430948 |
62 | Periconia epilithographicola | NR_157477 | 94.55 | Periconia sp. | MG543950 | 100 | Periconia sp. | OK430949 |
63 | Pezicula rhizophila | NR_155659 | 100 | Pezicula sp. | MN385513 | 100 | Pezicula sp. | OK430950 |
64 | Parastagonospora poagena | NR_168147 | 97.94 | Parastagonospora nodorum | MN313349 | 99.17 | Phaeosphaeriaceae | OK430951 |
65 | Phragmocephala garethjonessi | NR_147636 | 92.21 | Phragmocephala garethjonessi | MN660752 | 92.21 | Phragmocephala sp. A | OK430952 |
66 | Phragmocephala garethjonessi | NR_147636 | 90.2 | Phragmocephala atra | MN660752 | 90.61 | Phragmocephala sp. B | OK430953 |
67 | Phyllachora sp. | NR_156611 | 85 | Phyllachora graminis | AF257111 | 96.68 | Phyllachorales | OK430954 |
68 | Pleotrichocladium opacum | NR_155696 | 94.21 | Pleosporales | KY228531 | 99.58 | Pleosporales A | OK430955 |
69 | Camposporium multiseptatum | NR_171863 | 100 | Camposporium sp. | MN758889 | 100 | Pleosporales B | OK430956 |
70 | Anteaglonium rubescens | NR_164489 | 89.92 | Lophiostoma sp. | EU977287 | 93.17 | Pleosporales C | OK430957 |
71 | Pseudolachnella fusiformis | NR_154280 | 94.24 | Pseudolachnella fusiformis | AB934080 | 94.24 | Pseudolachnella sp. A | OK430958 |
72 | Pseudolachnella fusiformis | NR_154280 | 93.78 | Pseudolachnella fusiformis | AB934080 | 93.77 | Pseudolachnella sp. B | OK430959 |
73 | Puccinia aizazii | NR_158929 | 99.2 | Puccinia brachypodii | GQ457303 | 100 | Puccinia sp. | OK430960 |
74 | Plectosphaerella niemeijerarum | NR_156677 | 88.24 | Plectosphaerellaceae | MK762215 | 88.23 | Sordariomycetes A | OK430961 |
75 | Phaeoacrenonium cinereum | NR_ 132066 | 80.62 | Sordaryomycetes | KP050604 | 80.62 | Sordariomycetes B | OK430962 |
76 | Cordana pauciseptata | NR_154771 | 88.98 | Sordariales | UDB067041 | 96.69 | Sordariomycetes C | OK430963 |
77 | Neomyrmecridium guizhouense | NR_170024 | 82.45 | Sordariomycetes | LR865231 | 100 | Sordariomycetes D | OK430964 |
78 | Atractospora verruculosa | NR_153542 | 89.53 | Sordariales | EU754966 | 100 | Sordariomycetes E | OK430965 |
79 | Subulicistidium oberwinkleri | NR_159060 | 86.42 | Trechisporales | JF519283 | 100 | Trechisporales A | OK430966 |
80 | Subulicystidium oberwinkleri | NR_159060 | 80.53 | Trechisporales | UDB020436 | 83.77 | Trechisporales B | OK430967 |
81 | Trichoderma hispanicum | NR_138451 | 99.25 | Trichoderma koningii | MT781958 | 99.24 | Trichoderma sp. | OK430968 |
82 | Corinarius hadrocroceus | NR_131854 | 79.62 | Tricholomataceae | KX115676 | 100 | Tricholomataceae A | OK430969 |
83 | Mycena seminau | NR_154170 | 88.82 | Tricholomataceae | MH016642 | 99.67 | Tricholomataceae B | OK430970 |
84 | Phialocephala humicola | NR_103570 | 87.7 | Chaetosphaeriales | HM136627 | 100 | Unidentified A | OK430971 |
85 | Rhodosporidiobolus fluvialis | NR_077089 | 93.65 | Agaricomycetes | UDB0327559 | 100 | Unidentified B | OK430972 |
86 | Mycosymbioces mycenaphila | NR_137807 | 85.06 | Helotiales | UDB0779249 | 100 | Unidentified C | OK430973 |
87 | Mollisia monilioides | NR_171261 | 90.34 | Helotiales | KT203037 | 96.61 | Unidentified D | OK430974 |
88 | Linteromyces quintiniae | NR_171989 | 86.25 | Xylariales | MN218782 | 99.62 | Xylariales | OK430975 |
Appendix B
ROOT | RHIZOME | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Endophyte Taxon | Relative Abundance (%) | Reads | OTUs | Infected Plants | Relative Abundance (%) | Reads | OTUs | Infected Plants | ||||||||
LD | HD | LD | HD | LD | HD | LD | HD | LD | HD | LD | HD | LD | HD | LD | HD | |
Helotiaceae | 24.51 | 31.09 | 64,132 | 51,968 | 114 | 116 | 2 | 4 | 25.95 | 16.49 | 12,267 | 4897 | 94 | 18 | 2 | 4 |
Lachnum sp. A | 35.08 | 12.5 | 91,790 | 20,889 | 36 | 20 | 5 | 5 | 29.13 | 9.01 | 13,771 | 2676 | 5 | 7 | 4 | 4 |
Albotricha sp. A | 1.71 | 18.83 | 4465 | 31,473 | 7 | 6 | 3 | 3 | 5.23 | 50.58 | 2473 | 15,018 | 4 | 6 | 3 | 3 |
Helotiales A | 12.43 | 6.03 | 32,534 | 10,072 | 40 | 28 | 5 | 5 | 10.98 | 2.77 | 5188 | 823 | 25 | 1 | 2 | 3 |
Agaricales A | 3.55 | 9.65 | 9281 | 16,124 | 3 | 3 | 2 | 4 | 0.05 | 0 | 24 | 0 | 2 | 0 | 1 | 0 |
Mycena sp. A | 2.03 | 0.17 | 5323 | 289 | 10 | 2 | 4 | 1 | 20.88 | 0 | 9870 | 0 | 1 | 0 | 1 | 0 |
Mollisiaceae C | 4.17 | 0.45 | 10,913 | 745 | 2 | 1 | 4 | 1 | 0.42 | 0.04 | 198 | 13 | 2 | 1 | 1 | 1 |
Pleosporales A | 0.56 | 4.04 | 1476 | 6751 | 2 | 4 | 3 | 5 | 0 | 0.04 | 0 | 12 | 0 | 1 | 0 | 1 |
Glarea sp. | 0.41 | 3.94 | 1060 | 6589 | 2 | 1 | 2 | 1 | 0 | 0.29 | 0 | 86 | 0 | 1 | 0 | 1 |
Mollisiaceae B | 0.43 | 1.89 | 1118 | 3161 | 1 | 3 | 2 | 3 | 2.35 | 1.44 | 1111 | 429 | 1 | 3 | 2 | 2 |
Mollisiaceae D | 0.89 | 1.07 | 2330 | 1782 | 1 | 2 | 2 | 1 | 0.78 | 3.56 | 369 | 1056 | 1 | 2 | 2 | 2 |
Chaetosphaeriaceae | 1.76 | 0 | 4608 | 0 | 4 | 0 | 1 | 0 | 0.07 | 0 | 33 | 0 | 1 | 0 | 1 | 0 |
Mycena sp. B | 0 | 2.08 | 0 | 3479 | 0 | 3 | 0 | 1 | 0 | 3.34 | 0 | 993 | 0 | 1 | 0 | 1 |
Tricholomataceae B | 0 | 1.48 | 0 | 2474 | 0 | 1 | 0 | 2 | 0 | 4.21 | 0 | 1251 | 0 | 1 | 0 | 1 |
Lachnum sp. B | 0.38 | 1.27 | 1007 | 2119 | 11 | 7 | 4 | 4 | 0.87 | 0.14 | 411 | 43 | 1 | 1 | 1 | 1 |
Cantharellales | 1.3 | 0 | 3397 | 0 | 2 | 0 | 1 | 0 | ||||||||
Parasola sp. | 0 | 0.9 | 0 | 1503 | 0 | 1 | 0 | 1 | 0 | 5.81 | 0 | 1725 | 0 | 3 | 0 | 1 |
Unidentified A | 1.21 | 0.01 | 3174 | 19 | 2 | 1 | 1 | 1 | ||||||||
Ophiosphaerella sp. | 0.96 | 0.32 | 2513 | 535 | 2 | 1 | 2 | 1 | 0.11 | 0.06 | 50 | 17 | 1 | 1 | 1 | 1 |
Mollisiaceae A | 0.88 | 0.4 | 2309 | 666 | 4 | 3 | 4 | 5 | 0.03 | 0.28 | 13 | 83 | 1 | 1 | 1 | 1 |
Drechslera sp. | 0.03 | 1.43 | 87 | 2388 | 2 | 2 | 2 | 5 | ||||||||
Paracamarosporium sp. | 0.92 | 0 | 2419 | 0 | 1 | 0 | 4 | 0 | 0.06 | 0 | 28 | 0 | 1 | 0 | 2 | 0 |
Agaricales C | 0.58 | 0.07 | 1514 | 114 | 1 | 1 | 2 | 1 | ||||||||
Auriculariales | 0.5 | 0 | 1308 | 0 | 2 | 0 | 1 | 0 | ||||||||
Tricholomataceae A | 0.48 | 0 | 1266 | 0 | 1 | 0 | 1 | 0 | ||||||||
Unidentified B | 0.13 | 0.43 | 340 | 718 | 1 | 1 | 3 | 2 | 0.19 | 0.29 | 90 | 86 | 1 | 1 | 1 | 1 |
Pseudolachnella sp. B | 0.42 | 0.04 | 1097 | 72 | 1 | 1 | 3 | 2 | 0.11 | 0 | 51 | 0 | 1 | 0 | 1 | 0 |
Trichoderma sp. | 0.41 | 0.01 | 1076 | 15 | 1 | 1 | 2 | 1 | ||||||||
Didymosphaeriaceae | 0 | 0.58 | 0 | 963 | 0 | 2 | 0 | 1 | ||||||||
Conlarium sp. | 0.35 | 0 | 925 | 0 | 1 | 0 | 3 | 0 | 0.07 | 0 | 35 | 0 | 1 | 0 | 1 | 0 |
Helotiales C | 0.34 | 0 | 900 | 0 | 1 | 0 | 1 | 0 | ||||||||
Phragmocephala sp. A | 0.28 | 0 | 734 | 0 | 2 | 0 | 4 | 0 | ||||||||
Agaricales B | 0.26 | 0.02 | 675 | 32 | 2 | 1 | 1 | 1 | ||||||||
Menispora sp. | 0.27 | 0 | 702 | 0 | 1 | 0 | 2 | 0 | ||||||||
Cladophialophora sp. | 0.23 | 0.04 | 604 | 74 | 1 | 1 | 3 | 3 | 0.04 | 0 | 18 | 0 | 1 | 0 | 1 | 0 |
Pleosporales B | 0.11 | 0.2 | 299 | 341 | 1 | 2 | 1 | 2 | ||||||||
Pseudolachnella sp. A | 0.23 | 0.01 | 606 | 11 | 2 | 1 | 4 | 1 | ||||||||
Mortierellaceae | 0.11 | 0 | 283 | 0 | 2 | 0 | 1 | 0 | 0.43 | 0 | 201 | 0 | 3 | 0 | 1 | 0 |
Mollisiaceae F | 1.01 | 0 | 476 | 0 | 1 | 0 | 1 | 0 | ||||||||
Chalara sp. | 0.06 | 0.03 | 168 | 57 | 2 | 2 | 3 | 2 | 0.4 | 0.09 | 187 | 26 | 1 | 1 | 1 | 1 |
Sordariomycetes D | 0.17 | 0 | 435 | 0 | 1 | 0 | 1 | 0 | ||||||||
Helotiales B | 0.03 | 0 | 87 | 0 | 1 | 0 | 1 | 0 | 0.21 | 0.73 | 99 | 218 | 1 | 1 | 1 | 1 |
Agaricomycetes | 0.12 | 0 | 325 | 0 | 1 | 0 | 1 | 0 | ||||||||
Ascomycota B | 0.1 | 0 | 266 | 0 | 1 | 0 | 1 | 0 | 0.09 | 0 | 41 | 0 | 1 | 0 | 1 | 0 |
Mollisiaceae E | 0 | 0.13 | 0 | 216 | 0 | 1 | 0 | 1 | 0 | 0.31 | 0 | 91 | 0 | 1 | 0 | 1 |
Microdochium sp. | 0.07 | 0 | 187 | 0 | 1 | 0 | 3 | 0 | 0.25 | 0 | 119 | 0 | 1 | 0 | 1 | 0 |
Mortierella sp. | 0.12 | 0 | 305 | 0 | 2 | 0 | 1 | 0 | ||||||||
Sordariomycetes B | 0.11 | 0 | 297 | 0 | 1 | 0 | 1 | 0 | ||||||||
Pezicula sp. | 0 | 0.16 | 0 | 272 | 0 | 1 | 0 | 2 | ||||||||
Coccomyces sp. | 0.09 | 0.02 | 227 | 31 | 1 | 1 | 2 | 1 | ||||||||
Albotricha sp. B | 0 | 0.13 | 0 | 217 | 0 | 2 | 0 | 1 | 0 | 0.06 | 0 | 19 | 0 | 1 | 0 | 1 |
Leohumicola sp. | 0.06 | 0.03 | 166 | 57 | 1 | 1 | 4 | 2 | 0.03 | 0 | 13 | 0 | 1 | 0 | 1 | 0 |
Lachnum sp. C | 0.09 | 0 | 228 | 0 | 1 | 0 | 1 | 0 | ||||||||
Pleosporales C | 0 | 0.13 | 0 | 213 | 0 | 1 | 0 | 3 | ||||||||
Nectriaceae | 0.08 | 0 | 212 | 0 | 1 | 0 | 1 | 0 | ||||||||
Phragmocephala sp. B | 0.06 | 0.03 | 147 | 45 | 1 | 1 | 1 | 2 | ||||||||
Sordariomycetes C | 0 | 0.11 | 0 | 188 | 0 | 1 | 0 | 2 | ||||||||
Ascomycota A | 0.06 | 0 | 168 | 0 | 1 | 0 | 3 | 0 | ||||||||
Sordariomycetes E | 0.06 | 0 | 167 | 0 | 1 | 0 | 1 | 0 | ||||||||
Trechisporales B | 0 | 0.09 | 12 | 151 | 1 | 1 | 1 | 1 | ||||||||
Trechisporales A | 0.03 | 0 | 76 | 0 | 1 | 0 | 2 | 0 | 0 | 0.28 | 0 | 82 | 0 | 1 | 0 | 1 |
Agaricales D | 0.06 | 0 | 153 | 0 | 1 | 0 | 1 | 0 | ||||||||
Myrmecridium sp. | 0.06 | 0 | 149 | 0 | 1 | 0 | 2 | 0 | ||||||||
Dothideomycetes A | 0.04 | 0 | 117 | 0 | 1 | 0 | 1 | 0 | 0.06 | 0 | 30 | 0 | 1 | 0 | 1 | 0 |
Entoloma sp. | 0.06 | 0 | 144 | 0 | 1 | 0 | 1 | 0 | ||||||||
Falciphora sp. | 0.05 | 0 | 141 | 0 | 1 | 0 | 1 | 0 | ||||||||
Leotiomycetes | 0.05 | 0 | 139 | 0 | 1 | 0 | 1 | 0 | ||||||||
Mycena sp. D | 0.05 | 0.01 | 120 | 14 | 1 | 1 | 1 | 1 | ||||||||
Mycena sp. E | 0 | 0.08 | 0 | 133 | 0 | 1 | 0 | 1 | ||||||||
Unidentified D | 0.05 | 0 | 132 | 0 | 1 | 0 | 1 | 0 | ||||||||
Agaricales E | 0.05 | 0 | 128 | 0 | 1 | 0 | 1 | 0 | ||||||||
Dothideomycetes B | 0 | 0.08 | 0 | 127 | 0 | 1 | 0 | 1 | ||||||||
Unidentified C | 0.05 | 0 | 124 | 0 | 1 | 0 | 1 | 0 | ||||||||
Albotricha sp. C | 0.05 | 0 | 123 | 0 | 1 | 0 | 1 | 0 | ||||||||
Helotiales D | 0.05 | 0 | 121 | 0 | 1 | 0 | 1 | 0 | ||||||||
Neoascochyta sp. B | 0.01 | 0 | 17 | 0 | 1 | 0 | 1 | 0 | 0.22 | 0 | 102 | 0 | 1 | 0 | 3 | 0 |
Mycena sp. C | 0.03 | 0 | 86 | 0 | 1 | 0 | 1 | 0 | 0 | 0.07 | 0 | 22 | 0 | 1 | 0 | 1 |
Hyaloscyphaceae | 0.03 | 0.02 | 73 | 27 | 1 | 1 | 2 | 1 | ||||||||
Periconia sp. | 0.02 | 0 | 51 | 0 | 1 | 0 | 2 | 0 | ||||||||
Epicoccum sp. | 0 | 0 | 12 | 0 | 1 | 0 | 1 | 0 | 0 | 0.09 | 0 | 26 | 0 | 1 | 0 | 1 |
Phaeosphaeriaceae | 0 | 0.02 | 0 | 28 | 0 | 1 | 0 | 1 | ||||||||
Xylariales sp. | 0.04 | 0.01 | 105 | 12 | 1 | 1 | 2 | 1 | ||||||||
100 | 100 | 261673 | 167154 | 100 | 100 | 47268 | 29692 |
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Study Site | ARPEA | URKULU | |
---|---|---|---|
Type of Grassland | LD = Low Diversity | HD = High Diversity | |
General description | Location | −1°10′57″ W | –1°14′38″ W |
43°2′12″ N | 43°2′49″ N | ||
Soil classification (WRB) | Cambic Umbrisol | Dystric Cambisol | |
Altitude (m.a.s.l.) | 893 | 1256 | |
Slope (%) | 40 | 45 | |
Management | Burning recurrence | High 1–2 years | Low 6–7 years |
Type of burning | Large grassland areas | Bush-to-bush | |
Grazing level | Low to nonexistent | Moderate to high | |
B. rupestre cover (%) | >80% | <25% |
Match Taxon (NCBI) | Match Taxon (UNITE) | Taxon Proposed | GenBank Accession Number | |||||
---|---|---|---|---|---|---|---|---|
Accessio Number | Greatest Percentage Identity (%) | Accession Number | Greatest Percentage Identity (%) | |||||
1 | Lachnellula hyalina | NR_165202 | 90.11 | Albotricha sp. | HM136666 | 98.22 | Albotricha sp. | MW789554 |
2 | Codinaea paniculata | NR_166297 | 99.74 | Codinaea sp. | MT118230 | 99.74 | Codinaea sp. | MW789567 |
3 | Paracamarosporium sp. | NR_154318 | 94.28 | Paracamarosporium sp. | MT882131 | 97.6 | Didymosphaeriaceae | MW789559 |
4 | Drechslera sp. | NR_153992 | 94.43 | Drechslera sp. | UDB0174425 | 100 | Drechslera sp | MW789560 |
5 | Falciphora oryzae | NR_153972 | 96.69 | Falciphora sp. | UDB0162916 | 99.76 | Falciphora sp. | MW789558 |
6 | Glarea lozoyensis | NR_137138 | 96.18 | Glarea sp. | KF617491 | 99.58 | Helotiaceae | MW789565 |
7 | Ilyonectria leucospermi | NR_152889 | 99.36 | Ilyonectria crassa | MT294410 | 100 | Ilyonectria sp. | MW789566 |
8 | Lachnellula hualina | NR_165202 | 88.89 | Lachnum virgineum | MT133783 | 98.15 | Lachnum sp. | MW789564 |
9 | Microdochium phragmitis | NR_132916 | 100 | Microdochium phragmitis | MH861162 | 100 | Microdochium phragmitis | MW789562 |
10 | Mollisia asteliae | NR_173037 | 96.44 | Mollisia sp. | KJ188683 | 98.69 | Mollisia sp. | MW789555 |
11 | Phialocephala spaheroides | NR_121302 | 95.71 | Loramyces sp. | KF618060 | 99.36 | Mollisiaceae | MW789556 |
12 | Neoascochyta dactylidis | NR_170041 | 100 | Neoascochyta sp. | MT185527 | 100 | Neoascochyta sp. | MW789561 |
13 | Omnidemptus graminis | NR_164058 | 100 | Omnidemptus graminis | MK487758 | 100 | Omnidemptus graminis | MW789553 |
14 | Phialocephala sphaeroides | NR_121302 | 89 | Phialocephala sp. | JN995646 | 98.87 | Phialocephala sp. | MW789563 |
15 | Paraphaeosphaeria michotii | NR_155640 | 91.41 | Pleosporales | MN450621 | 100 | Pleosporales | MW789557 |
Type of Grassland | Tissue | ||||||
---|---|---|---|---|---|---|---|
Shoot | Rhizome | Root | |||||
Metabarcoding method | Reads | LD | 313,621 | 4680 | 47,268 | 261,673 | |
HD | 200,050 | 3204 | 29,692 | 167,154 | |||
Total | 513,671 | 7884 | 76,960 | 428,827 | |||
OTUs | LD | 316 | 12 | 165 | 305 | ||
HD | 246 | 11 | 58 | 236 | |||
Total | 352 | 19 | 197 | 340 | |||
Taxa | LD | 75 | 10 | 27 | 69 | ||
HD | 52 | 10 | 23 | 45 | |||
Total | 88 | 15 | 37 | 82 | |||
Culture method | Taxa | LD | 10 | 2 | 3 | 6 | |
HD | 8 | 1 | 3 | 5 | |||
Total | 15 | 2 | 5 | 11 |
Sample | Culture Method | Match Methods | Metabarcoding | |||
---|---|---|---|---|---|---|
Isolated Taxa | Taxa | OTUs | Reads | |||
Shoot LD | 1 | Neoascochyta sp. | ✓ | 5 | 5 | 233 |
2 | Omnidemptus graminis | × | 5 | 6 | 1639 | |
3 | Omnidemptus graminis | × | 7 | 9 | 1619 | |
4 | Omnidemptus graminis | × | 3 | 3 | 207 | |
5 | × | 4 | 4 | 982 | ||
Shoot HD | 6 | × | 2 | 2 | 229 | |
7 | Omnidemptus graminis | × | 2 | 2 | 37 | |
8 | Omnidemptus graminis | × | 5 | 5 | 644 | |
9 | Omnidemptus graminis | × | 1 | 1 | 13 | |
10 | × | 3 | 3 | 2281 | ||
Rhizome LD | 1 | × | 8 | 102 | 12,546 | |
2 | × | 11 | 21 | 24,377 | ||
3 | Didymosphaeriaceae | × | 4 | 6 | 1312 | |
Helotiaceae | ✓ | |||||
4 | × | 5 | 7 | 831 | ||
5 | Mollisiaceae | ✓ | 12 | 41 | 8202 | |
Rhizome HD | 6 | Helotiaceae | ✓ | 6 | 22 | 5621 |
7 | Helotiaceae | ✓ | 3 | 4 | 267 | |
8 | Phialocephala sp. | × | 11 | 17 | 15,380 | |
9 | × | 4 | 5 | 2035 | ||
10 | Microdochium phragmitis | × | 11 | 18 | 6389 | |
Root LD | 1 | Didymosphaeriaceae | × | 15 | 180 | 49,606 |
2 | Falciphora sp. | ✓ | 29 | 53 | 40,482 | |
Codinaea sp. | × | |||||
3 | Didymosphaeriaceae | × | 27 | 184 | 70,132 | |
4 | Mollisia sp. | × | 34 | 73 | 52,335 | |
5 | Pleosporales | × | 31 | 95 | 49,118 | |
Didymosphaeriaceae | × | |||||
Lachnum sp. | ✓ | |||||
Root HD | 6 | Helotiaceae | ✓ | 18 | 141 | 62,044 |
7 | Mollisiaceae | ✓ | 20 | 116 | 23,703 | |
8 | Albotricha sp. | ✓ | 16 | 32 | 12,379 | |
9 | Albotricha sp. | ✓ | 20 | 55 | 47,814 | |
10 | Drechslera sp. | ✓ | 17 | 59 | 21,214 | |
Ilyonectria sp. | × |
ROOT | RHIZOME | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Endophyte Taxon | Relative Abundance (%) | Reads | OTUs | Infected Plants | Relative Abundance (%) | Reads | OTUs | Infected Plants | ||||||||
LD | HD | LD | HD | LD | HD | LD | HD | LD | HD | LD | HD | LD | HD | LD | HD | |
Helotiaceae | 24.51 | 31.09 | 64,132 | 51,968 | 114 | 116 | 2 | 4 | 25.95 | 16.49 | 12,267 | 4897 | 94 | 18 | 2 | 4 |
Lachnum sp. A | 35.08 | 12.5 | 91,790 | 20,889 | 36 | 20 | 5 | 5 | 29.13 | 9.01 | 13,771 | 2676 | 5 | 7 | 4 | 4 |
Albotricha sp. A | 1.71 | 18.83 | 4465 | 31,473 | 7 | 6 | 3 | 3 | 5.23 | 50.58 | 2473 | 15,018 | 4 | 6 | 3 | 3 |
Helotiales A | 12.43 | 6.03 | 32,534 | 10,072 | 40 | 28 | 5 | 5 | 10.98 | 2.77 | 5188 | 823 | 25 | 1 | 2 | 3 |
Agaricales A | 3.55 | 9.65 | 9281 | 16,124 | 3 | 3 | 2 | 4 | 0.05 | 0 | 24 | 0 | 2 | 0 | 1 | 0 |
Mycena sp. A | 2.03 | 0.17 | 5323 | 289 | 10 | 2 | 4 | 1 | 20.88 | 0 | 9870 | 0 | 1 | 0 | 1 | 0 |
Mollisiaceae C | 4.17 | 0.45 | 10,913 | 745 | 2 | 1 | 4 | 1 | 0.42 | 0.04 | 198 | 13 | 2 | 1 | 1 | 1 |
Pleosporales A | 0.56 | 4.04 | 1476 | 6751 | 2 | 4 | 3 | 5 | 0 | 0.04 | 0 | 12 | 0 | 1 | 0 | 1 |
Glarea sp. | 0.41 | 3.94 | 1060 | 6589 | 2 | 1 | 2 | 1 | 0 | 0.29 | 0 | 86 | 0 | 1 | 0 | 1 |
Mollisiaceae B | 0.43 | 1.89 | 1118 | 3161 | 1 | 3 | 2 | 3 | 2.35 | 1.44 | 1111 | 429 | 1 | 3 | 2 | 2 |
Mollisiaceae D | 0.89 | 1.07 | 2330 | 1782 | 1 | 2 | 2 | 1 | 0.78 | 3.56 | 369 | 1056 | 1 | 2 | 2 | 2 |
Chaetosphaeriaceae | 1.76 | 0 | 4608 | 0 | 4 | 0 | 1 | 0 | 0.07 | 0 | 33 | 0 | 1 | 0 | 1 | 0 |
Mycena sp. B | 0 | 2.08 | 0 | 3479 | 0 | 3 | 0 | 1 | 0 | 3.34 | 0 | 993 | 0 | 1 | 0 | 1 |
Tricholomataceae B | 0 | 1.48 | 0 | 2474 | 0 | 1 | 0 | 2 | 0 | 4.21 | 0 | 1251 | 0 | 1 | 0 | 1 |
Lachnum sp. B | 0.38 | 1.27 | 1007 | 2119 | 11 | 7 | 4 | 4 | 0.87 | 0.14 | 411 | 43 | 1 | 1 | 1 | 1 |
Cantharellales | 1.3 | 0 | 3397 | 0 | 2 | 0 | 1 | 0 | ||||||||
Parasola sp. | 0 | 0.9 | 0 | 1503 | 0 | 1 | 0 | 1 | 0 | 5.81 | 0 | 1725 | 0 | 3 | 0 | 1 |
Unidentified A | 1.21 | 0.01 | 3174 | 19 | 2 | 1 | 1 | 1 | ||||||||
Ophiosphaerella sp. | 0.96 | 0.32 | 2513 | 535 | 2 | 1 | 2 | 1 | 0.11 | 0.06 | 50 | 17 | 1 | 1 | 1 | 1 |
Mollisiaceae A | 0.88 | 0.4 | 2309 | 666 | 4 | 3 | 4 | 5 | 0.03 | 0.28 | 13 | 83 | 1 | 1 | 1 | 1 |
Drechslera sp. | 0.03 | 1.43 | 87 | 2388 | 2 | 2 | 2 | 5 |
SHOOT | ||||||||
---|---|---|---|---|---|---|---|---|
Endophyte Taxon | Relative Abundance (%) | Reads | OTUs | Infected Plants | ||||
LD | HD | LD | HD | LD | HD | LD | HD | |
Phaeosphaeriaceae | 34.08 | 58.80 | 1595 | 1884 | 2 | 1 | 4 | 2 |
Phyllachorales | 20.49 | 0 | 959 | 0 | 1 | 0 | 4 | 0 |
Puccinia sp. | 16.05 | 0 | 751 | 0 | 3 | 0 | 1 | 0 |
Neoascochyta sp. A | 14.94 | 0.53 | 699 | 17 | 1 | 1 | 4 | 1 |
Sordariomycetes A | 0 | 17.45 | 0 | 559 | 0 | 1 | 0 | 1 |
Mycosphaerellaceae | 0 | 12.73 | 0 | 408 | 1 | 0 | 0 | 1 |
Microdochium sp. | 5.58 | 1.59 | 261 | 51 | 1 | 1 | 4 | 1 |
Dothideales | 3.65 | 0 | 171 | 0 | 1 | 0 | 2 | 0 |
Ophiosphaerella sp. | 0 | 4.68 | 0 | 150 | 0 | 1 | 0 | 1 |
Epicoccum sp. | 2.01 | 0.75 | 94 | 24 | 1 | 1 | 1 | 1 |
Helotiaceae | 1.41 | 1.56 | 66 | 50 | 1 | 2 | 2 | 3 |
Periconia sp. | 1.56 | 0 | 73 | 0 | 1 | 0 | 1 | 0 |
Lachnum sp. A | 0 | 1.28 | 0 | 41 | 0 | 1 | 0 | 1 |
Phragmocephala sp. B | 0 | 0.63 | 0 | 20 | 1 | 0 | 0 | 1 |
Unidentified C | 0.23 | 0 | 11 | 0 | 1 | 0 | 1 | 0 |
100 | 100 | 4680 | 3204 |
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Durán, M.; San Emeterio, L.; Canals, R.M. Comparison of Culturing and Metabarcoding Methods to Describe the Fungal Endophytic Assemblage of Brachypodium rupestre Growing in a Range of Anthropized Disturbance Regimes. Biology 2021, 10, 1246. https://doi.org/10.3390/biology10121246
Durán M, San Emeterio L, Canals RM. Comparison of Culturing and Metabarcoding Methods to Describe the Fungal Endophytic Assemblage of Brachypodium rupestre Growing in a Range of Anthropized Disturbance Regimes. Biology. 2021; 10(12):1246. https://doi.org/10.3390/biology10121246
Chicago/Turabian StyleDurán, María, Leticia San Emeterio, and Rosa Maria Canals. 2021. "Comparison of Culturing and Metabarcoding Methods to Describe the Fungal Endophytic Assemblage of Brachypodium rupestre Growing in a Range of Anthropized Disturbance Regimes" Biology 10, no. 12: 1246. https://doi.org/10.3390/biology10121246