The relative impact of site, season, plant compartment and health status were different for each tree species these differences can be interpreted as a matter of water availability. Host species was the strongest driver of fungal community structure and composition, while the host health status was the weakest. However, we detected additional heterogeneity and greater richness with culture‐free methods. The diversity patterns inferred through the metabarcoding analysis were similar to those obtained through culture‐dependent approaches. In this study, we used next‐generation sequencing to characterize sapwood‐inhabiting fungal communities in North Patagonian Nothofagus forests and assessed patterns of diversity of taxa and ecological guilds across climatic, site and host variables (health condition and compartment) as a contribution to Nothofagus autecology. Little is known about the ecology of forest pathology and related microbial communities in temperate forests of the southern hemisphere. The complex ecological interactions among pathogens, microbial communities, tree host, and environment are important drivers of forest dynamics. Global forests are increasingly threatened by altered climatic conditions and increased attacks by pests and pathogens.
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