Changes in fungal communities associated with healthy and diseased pea roots were investigated using deep amplicon pyrosequencing in three spatial compartments: roots, rhizosphere, and surrounding soil. Thirty root systems were collected from three fields, half of which showing clear symptoms of root rot. In total, 500 461 internal transcribed spacer-1 sequences were obtained that were clustered into 123 (roots), 271 (rhizosphere), and 440 (bulk soil) nonsingleton operational taxonomic units (OTUs). Species richness was highest in bulk soils and lowest in roots; however, no notable differences in richness were observed between samples associated with diseased and healthy roots. Health status and field both had significant effects on fungal community structures in roots, whereas only field had significant effects on communities in rhizosphere and bulk soils. Indicator species analysis across the three fields identified a number of OTUs that were more abundant in healthy roots. Pathogens such as Fusarium oxysporum were abundant in diseased roots in some fields. Patterns of disease and causal agents of root rot were different among the three fields, which were also reflected in fungal communities. In conclusion, health status of roots was only vaguely reflected in rhizosphere and bulk soil fungal communities, whereas health status was more important for shaping root communities.
F E M S Microbiology Ecology, 2012, Vol 82, Issue 3, p. 736-745