TABLE 2.
OTUs with the highest sequence counts after rarefaction, ranked from most to least abundant, with the identity and confidence of the closest match to each ITS2 sequence according to the Warcup data set (93)a
| Phylum | Subphylum | Class | Order | Family | Species | Confidence | Possible guild (reference) | OTU | No. of sequences |
|---|---|---|---|---|---|---|---|---|---|
| Basidiomycota | Unknown | Unassigned | 0.61 | Unknown | 1880 | 238,381 | |||
| Ascomycota | Pezizomycotina | Dothideomycetes | Pleosporales | Pleosporaceae | Edenia gomezpompae | 0.86 | Endophyte (101) | 9344 | 230,312 |
| Ascomycota | Pezizomycotina | Incertae sedis | Incertae sedis | Incertae sedis | Knufia sp. | 0.75 | Plant pathogen-saprotroph (102) | 6468 | 174,704 |
| Ascomycota | Pezizomycotina | Sordariomycetes | Xylariales | Unknown | Unassigned | 0.88 | Unknown | 5805 | 117,117 |
| Ascomycota | Pezizomycotina | Dothideomycetes | Incertae sedis | Incertae sedis | Rhizopycnis vagum | 1 | Endophyte-plant pathogen (103) | 8402 | 104,774 |
| Ascomycota | Pezizomycotina | Sordariomycetes | Hypocreales | Nectriaceae | Fusarium oxysporum | 1 | Plant pathogen-saprotroph (104) | 9601 | 100,613 |
| Ascomycota | Pezizomycotina | Incertae sedis | Incertae sedis | Incertae sedis | Campylospora parvula | 1 | Saprotroph (105) | 5752 | 78,721 |
| Ascomycota | Pezizomycotina | Unknown | Unassigned | 0.67 | Unknown | 1891 | 68,607 | ||
| Basidiomycota | Unknown | Unassigned | 0.53 | Unknown | 2630 | 59,736 | |||
| Basidiomycota | Agaricomycotina | Agaricomycetes | Agaricales | Mycenaceae | Mycena sp. | 0.82 | Plant pathogen-saprotroph (41) | 1767 | 58,566 |
| Ascomycota | Pezizomycotina | Leotiomycetes | Helotiales | Unknown | Unassigned | 0.56 | Unknown | 10037 | 48,594 |
| Ascomycota | Pezizomycotina | Unknown | Unassigned | 0.76 | Unknown | 1255 | 47,714 | ||
| Ascomycota | Pezizomycotina | Sordariomycetes | Hypocreales | Nectriaceae | F. oxysporum | 0.77 | Plant pathogen-saprotroph | 9265 | 42,491 |
| Basidiomycota | Unknown | Unassigned | 0.65 | Unknown | 1806 | 32,492 | |||
| Ascomycota | Pezizomycotina | Sordariomycetes | Unknown | Unassigned | 0.70 | Unknown | 9359 | 27,181 | |
| Ascomycota | Pezizomycotina | Sordariomycetes | Hypocreales | Nectriaceae | Cylindrocarpon pauciseptatum | 0.99 | Plant pathogen (106) | 7563 | 26,079 |
| Basidiomycota | Agaricomycotina | Agaricomycetes | Boletales | Sclerodermataceae | Scleroderma | 0.82 | Ectomycorrhiza-saprotroph (107) | 607 | 25,638 |
| Ascomycota | Pezizomycotina | Incertae sedis | Incertae sedis | Incertae sedis | Dokmaia monthadangii | 1 | Endophyte-saprotroph (108) | 9893 | 23,968 |
| Ascomycota | Pezizomycotina | Incertae sedis | Incertae sedis | Incertae sedis | Knufia sp. | 0.82 | Plant pathogen-saprotroph | 6670 | 23,646 |
| Ascomycota | Pezizomycotina | Incertae sedis | Incertae sedis | Incertae sedis | Knufia sp. | 0.88 | Plant pathogen-saprotroph | 7039 | 23,211 |
| Unknown | Unassigned | 1 | Unknown | 599 | 21,659 | ||||
| Ascomycota | Pezizomycotina | Leotiomycetes | Helotiales | Unknown | Unassigned | 0.74 | Unknown | 10151 | 20,063 |
| Ascomycota | Pezizomycotina | Dothideomycetes | Pleosporales | Incertae sedis | Phoma putaminum | 0.92 | Plant pathogen-saprotroph (109) | 8246 | 19,052 |
| Basidiomycota | Agaricomycotina | Agaricomycetes | Agaricales | Unknown | Unassigned | 0.78 | Unknown | 368 | 16,762 |
| Basidiomycota | Agaricomycotina | Agaricomycetes | Agaricales | Mycenaceae | Mycena sp. | 0.64 | Plant pathogen-saprotroph | 2148 | 16,495 |
| Ascomycota | Pezizomycotina | Sordariomycetes | Incertae sedis | Plectosphaerellaceae | Plectosphaerella cucumerina | 0.94 | Plant pathogen (110) | 6360 | 16,470 |
| Ascomycota | Pezizomycotina | Sordariomycetes | Hypocreales | Clavicipitaceae | Pochonia chlamydosporia | 0.58 | Animal pathogen (111) | 3444 | 15,452 |
| Ascomycota | Pezizomycotina | Incertae sedis | Incertae sedis | Incertae sedis | Knufia sp. | 0.73 | Plant pathogen-saprotroph | 7477 | 15,327 |
| Ascomycota | Pezizomycotina | Incertae sedis | Incertae sedis | Incertae sedis | Knufia sp. | 0.69 | Plant pathogen-saprotroph | 6851 | 14,536 |
| Basidiomycota | Agaricomycotina | Agaricomycetes | Cantharellales | Ceratobasidiaceae | Ceratobasidium sp. | 0.97 | Ectomycorrhiza-plant pathogen (1, 42) | 1265 | 14,129 |
| Basidiomycota | Agaricomycotina | Agaricomycetes | Unknown | Unassigned | 0.72 | Unknown | 1614 | 13,874 | |
| Basidiomycota | Unknown | Unassigned | 0.60 | Unknown | 2317 | 12,474 | |||
| Basidiomycota | Unknown | Unassigned | 0.59 | Unknown | 3165 | 12,142 | |||
| Basidiomycota | Agaricomycotina | Agaricomycetes | Atheliales | Atheliaceae | Cristinia helvetica | 0.97 | Saprotroph (112) | 1183 | 11,952 |
| Ascomycota | Pezizomycotina | Sordariomycetes | Unknown | Unassigned | 0.59 | Unknown | 6182 | 11,762 | |
| Basidiomycota | Agaricomycotina | Agaricomycetes | Unknown | Unassigned | 0.67 | Unknown | 3641 | 11,521 | |
| Basidiomycota | Agaricomycotina | Agaricomycetes | Agaricales | Mycenaceae | Mycena sp. | 0.84 | Plant pathogen-saprotroph | 718 | 11,479 |
| Ascomycota | Pezizomycotina | Pezizomycetes | Pezizales | Sarcoscyphaceae | Unassigned | 0.79 | Unknown | 5955 | 11,425 |
| Basidiomycota | Agaricomycotina | Agaricomycetes | Agaricales | Porotheleaceae | Phloeomana speirea | 0.71 | Plant pathogen-saprotroph (113) | 3755 | 11,222 |
| Ascomycota | Pezizomycotina | Sordariomycetes | Hypocreales | Incertae sedis | Nectria mauritiicola | 0.57 | Plant pathogen-saprotroph (114) | 6887 | 11,204 |
| Basidiomycota | Agaricomycotina | Agaricomycetes | Cantharellales | Ceratobasidiaceae | Ceratobasidium sp. | 0.72 | Ectomycorrhiza-plant pathogen | 990 | 10,687 |
| Ascomycota | Pezizomycotina | Sordariomycetes | Hypocreales | Nectriaceae | C. pauciseptatum | 0.99 | Plant pathogen | 7576 | 10,575 |
| Basidiomycota | Agaricomycotina | Agaricomycetes | Cantharellales | Ceratobasidiaceae | Ceratobasidium sp. | 0.89 | Ectomycorrhiza-plant pathogen | 1068 | 10,130 |
| Ascomycota | Pezizomycotina | Incertae sedis | Incertae sedis | Incertae sedis | Knufia sp. | 0.82 | Plant pathogen-saprotroph | 6859 | 10,124 |
| Ascomycota | Pezizomycotina | Dothideomycetes | Pleosporales | Unknown | Unassigned | 0.84 | Unknown | 8625 | 10,058 |
| Ascomycota | Pezizomycotina | Dothideomycetes | Capnodiales | Mycosphaerellaceae | Cladosporium perangustum | 1 | Endophyte-plant pathogen (115, 116) | 9431 | 10,049 |
a
Possible guild was determined from published literature. Only the 46 OTUs with sequence counts of >10,000 are shown; of these, only OTU 6468 differed in abundance between coffee roots of conventionally managed and organic fields.