TABLE 3.
Fungal OTUs that differed in abundance between coffee roots from conventionally managed and organic fields by three-way ANOVA, with year, region, and field type as main effects and all interactions at an α of 0.05a
| Phylum | Subphylum | Class | Order | Family | Species | Conf | Possible guild | OTU | No. of occurrences by field type (mean ± SE) |
F1,14 | FDR P | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Conventional | Organic | |||||||||||
| Ascomycota | Pezizomycotina | Dothideomycetes | Pleosporales | Unknown | Unassigned | 0.52 | Unknown | 9400 | 9 ± 4 | 155 ± 63 | 26.66 | 0.0102 |
| Ascomycota | Pezizomycotina | Eurotiomycetes | Chaetothyriales | Herpotrichiellaceae | Exophiala sp. | 1 | S | 3736 | 3 ± 3 | 286 ± 142 | 47.92 | 0.0016 |
| Ascomycota | Pezizomycotina | Eurotiomycetes | Chaetothyriales | Herpotrichiellaceae | Exophiala sp. | 1 | S | 4272 | 9 ± 6 | 176 ± 74 | 17.00 | 0.0333 |
| Ascomycota | Pezizomycotina | Eurotiomycetes | Chaetothyriales | Herpotrichiellaceae | Exophiala pisciphila | 0.97 | S | 4246 | 473 ± 77 | 96 ± 48 | 27.36 | 0.0096 |
| Ascomycota | Pezizomycotina | Incertae sedis | Campylospora parvula | 1 | S | 7040 | 3 ± 2 | 510 ± 334 | 17.62 | 0.0301 | ||
| Ascomycota | Pezizomycotina | Incertae sedis | Dokmaia monthadangii | 1 | Endophyte | 9531 | 23 ± 9 | 187 ± 64 | 15.93 | 0.0389 | ||
| Ascomycota | Pezizomycotina | Incertae sedis | Knufia sp. | 0.75 | S-PP | 6468 | 10,866 ± 2,241 | 1,028 ± 255 | 67.57 | 0.0004 | ||
| Ascomycota | Pezizomycotina | Incertae sedis | Knufia sp. | 0.82 | S-PP | 7025 | 37 ± 8 | 2 ± 1 | 80.45 | 0.0003 | ||
| Ascomycota | Pezizomycotina | Incertae sedis | Knufia sp. | 0.63 | S-PP | 7027 | 36 ± 8 | 3 ± 1 | 78.26 | 0.0003 | ||
| Ascomycota | Pezizomycotina | Incertae sedis | Knufia sp. | 0.72 | S-PP | 7053 | 66 ± 15 | 8 ± 3 | 43.92 | 0.0019 | ||
| Ascomycota | Pezizomycotina | Incertae sedis | Knufia sp. | 0.71 | S-PP | 7059 | 85 ± 19 | 9 ± 3 | 79.82 | 0.0003 | ||
| Ascomycota | Pezizomycotina | Incertae sedis | Knufia sp. | 0.71 | S-PP | 7070 | 38 ± 8 | 3 ± 1 | 45.97 | 0.0017 | ||
| Ascomycota | Pezizomycotina | Sordariomycetes | Hypocreales | Incertae sedis | Acremonium furcatum | 0.99 | Multiple | 6073 | 7 ± 4 | 78 ± 33 | 24.18 | 0.0129 |
| Ascomycota | Pezizomycotina | Sordariomycetes | Hypocreales | Incertae sedis | Acremonium stromaticum | 0.67 | Multiple | 6237 | 4 ± 2 | 43 ± 19 | 31.06 | 0.0072 |
| Ascomycota | Pezizomycotina | Sordariomycetes | Hypocreales | Incertae sedis | Myrothecium cinctum | 0.98 | S | 8768 | 5 ± 2 | 58 ± 25 | 20.80 | 0.0192 |
| Ascomycota | Pezizomycotina | Sordariomycetes | Hypocreales | Incertae sedis | Myrothecium roridum | 1 | S | 4618 | 5 ± 3 | 170 ± 82 | 23.27 | 0.0146 |
| Ascomycota | Pezizomycotina | Sordariomycetes | Hypocreales | Nectriaceae | Cylindrocarpon pauciseptatum | 0.99 | PP | 7563 | 459 ± 176 | 2,190 ± 646 | 15.30 | 0.0416 |
| Ascomycota | Pezizomycotina | Sordariomycetes | Hypocreales | Nectriaceae | Fusarium equiseti | 0.92 | S-PP | 9134 | 108 ± 37 | 481 ± 233 | 15.49 | 0.0413 |
| Ascomycota | Pezizomycotina | Sordariomycetes | Hypocreales | Nectriaceae | Unknown | 0.6 | S | 5297 | 43 ± 22 | 0 ± 0 | 14.24 | 0.0493 |
| Ascomycota | Pezizomycotina | Sordariomycetes | Incertae sedis | Myrmecridium schulzeri | 0.98 | S | 9604 | 20 ± 5 | 108 ± 36 | 19.20 | 0.0234 | |
| Ascomycota | Pezizomycotina | Sordariomycetes | Sordariales | Chaetomiaceae | Unassigned | 0.58 | Unknown | 8505 | 44 ± 24 | 0 ± 0 | 19.19 | 0.0234 |
| Ascomycota | Pezizomycotina | Sordariomycetes | Unknown | Unassigned | 0.84 | Unknown | 5069 | 7 ± 7 | 62 ± 30 | 21.69 | 0.0177 | |
| Ascomycota | Pezizomycotina | Sordariomycetes | Unknown | Unassigned | 0.59 | Unknown | 6182 | 724 ± 149 | 147 ± 71 | 15.72 | 0.0402 | |
| Ascomycota | Pezizomycotina | Sordariomycetes | Unknown | Unassigned | 0.52 | Unknown | 7523 | 50 ± 22 | 1 ± 0 | 17.12 | 0.0330 | |
| Ascomycota | Pezizomycotina | Unknown | Unassigned | 1 | Unknown | 3916 | 1 ± 1 | 86 ± 30 | 71.98 | 0.0003 | ||
| Ascomycota | Pezizomycotina | Unknown | Unassigned | 0.97 | Unknown | 4271 | 2 ± 1 | 99 ± 57 | 94.53 | 0.0003 | ||
| Ascomycota | Pezizomycotina | Unknown | Unassigned | 0.6 | Unknown | 7282 | 2 ± 2 | 62 ± 32 | 24.44 | 0.0129 | ||
| Basidiomycota | Agaricomycotina | Agaricomycetes | Agaricales | Agaricaceae | Unknown | 0.71 | S | 3456 | 0 ± 0 | 68 ± 55 | 19.77 | 0.0220 |
| Basidiomycota | Agaricomycotina | Agaricomycetes | Agaricales | Mycenaceae | Mycena sp. | 0.87 | S-PP | 2014 | 170 ± 110 | 0 ± 0 | 73.55 | 0.0003 |
| Basidiomycota | Agaricomycotina | Agaricomycetes | Cantharellales | Ceratobasidiaceae | Ceratobasidium | 0.96 | PP-Ecto | 972 | 3 ± 3 | 75 ± 50 | 24.02 | 0.0129 |
| Glomeromycota | Glomeromycotina | Glomeromycetes | Diversisporales | Gigasporaceae | Gigaspora sp. | 0.87 | AM | 5119 | 82 ± 30 | 0 ± 0 | 25.32 | 0.0119 |
| Glomeromycota | Glomeromycotina | Glomeromycetes | Diversisporales | Gigasporaceae | Gigaspora sp. | 0.71 | AM | 5518 | 115 ± 45 | 0 ± 0 | 17.21 | 0.0328 |
| Glomeromycota | Glomeromycotina | Glomeromycetes | Diversisporales | Gigasporaceae | Gigaspora margarita | 0.95 | AM | 5234 | 205 ± 86 | 0 ± 0 | 15.97 | 0.0389 |
| Unknown | Unassigned | 1 | Unknown | 1774 | 9 ± 5 | 367 ± 185 | 22.27 | 0.0161 | ||||
a
Only OTUs with sequence counts of >500 and found in >3 coffee fields were included in the analysis. Possible guild was as assigned by FUNGuild, with the identity and confidence (Conf) of the closest match to each ITS2 sequence according to the Warcup data set (93). S, saprotroph; S-PP, saprotroph-plant pathogen; AM, arbuscular mycorrhizal; Ecto, ectomycorrhizal; FDR P, false-discovery rate P value.