Deep sequencing across multiple host species tests pine-endophyte specificity

Premise Foliar fungal endophytes vary in their distributions across landscapes or plant host taxa, indicative of specialized ecologies and host specific adaptations. Accounts of specialization, however, depend on the taxonomic breadth and geographic range of the host plants included in each study. A broad region-scale study or deep sampling of diverse potential host species still remains relatively rare but is becoming increasingly possible with high-throughput sequencing. Methods Amplicon sequencing was used to rapidly identify the fungal endophytic community among six pine (Pinus, Pinaceae) species co-occurring across northeastern United States and to test for site and host specialization. We focused on the endophytic genus Lophodermium (Rhytismataceae), whose species' members are thought to specialize on different pine species, to test if amplicon sequencing could rapidly verify previously implied or discover new patterns of host specificity. Results While amplicon sequencing could analyze more samples at greater depths and recover greater numbers of unique Lophodermium taxa than when endophyte communities were surveyed with traditional culturing methods, patterns of specialization were not better supported. This may be because amplicon sequencing can indiscriminately capture non-host specific organisms found incidentally from plant tissues or because we have overestimated host-specificity in the past with biased culturing techniques. Conclusions Amplicon sequencing can quickly identify patterns of host specificity by allowing large-scale surveys but has limitations in quantifying the level of intimacy of these relationships.

Automated summary

Amplicon sequencing was used to rapidly identify the fungal endophytic community among six pine species in the northeastern United States and detect patterns of specialization. While this technique allowed for large-scale surveys, it had limitations in quantifying the intimacy of host specificity relationships.