Root systems of declining conifer seedlings are colonised by a highly diverse fungal community

Fungi of roots of declining pine and spruce seedlings were assessed by pure culture isolations and direct sequencing. The isolation from 1440 roots of 480 seedlings (240 per each tree species) yielded 1110 isolates which, based on mycelial morphology and ITS rDNA sequences, were found to represent 87 distinct taxa. Direct ITS rDNA sequencing from decayed sections of 140 roots (70 per each tree species) yielded 160 sequences representing 58 taxa. In respect to the amount of examined roots, direct sequencing revealed significantly larger fungal diversity (chi-squared test; p<0.0001). A total of 131 taxa were found, 92 of which (70.2 %) were identified at least to a genus level. Only 14 of the total number (10.7 %) were detected by both methods, while 73 (55.7 %) were detected exclusively by isolation, and 44 (33.6 %) exclusively by sequencing. Fungi most commonly isolated were the pat-hogens Fusarium oxysporum (25.6 %) and Nectria radici-cola (14.9 %). On the contrary, direct sequencing most fre-quently revealed presence of the endophyte Phialocephala fortinii (33.1 %) and the unidentified sp.NS234A2 (10.0 %). Our results demonstrate that a diverse fungal community inhabits roots of declining conifer seedlings, and that pure culture isolations combined with direct sequencing provides complementary data in studies of fungal communities.