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ARS Home » Southeast Area » Fort Pierce, Florida » U.S. Horticultural Research Laboratory » Subtropical Plant Pathology Research » Research » Publications at this Location » Publication #216597

Title: Assessment of fungal communities in soil and tomato roots subjected to diverse land and crop management systems

item Wu, Tiehang
item Chellemi, Daniel
item Graham, Jim
item Rosskopf, Erin

Submitted to: Soil Biology and Biochemistry
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/1/2007
Publication Date: 6/1/2008
Citation: Wu, T., Chellemi, D.O., Graham, J., Rosskopf, E.N. 2008. Assessment of fungal communities in soil and tomato roots subjected to diverse land and crop management systems. Soil Biology and Biochemistry. 40:1967-1970.

Interpretive Summary: Soil fungi are a key biological component in the regulation of terrestrial ecosystems. Studies on diversity and composition of soil fungal communities can further the understanding of ecosystem-level processes and thus, the development of sustainable agricultural systems. In this study, the effects of agricultural land management practices on the structure of soil fungal communities was coupled with measurements on a functional subset, communities of root colonizing fungi on tomato (Lycopersicon esculentum) cultivated in treated soils. Culture-dependent colony counting was employed to characterize communities of root colonizing fungi (the functional subset) and LH-PCR to discriminate soil fungal communities. The differences in whole soil fungal communities and a functional subset of root colonizing fungi under alternative agricultural land management practices were evaluated by PCR-based molecular methods and culture-dependent colony counting. Characterization of the soil fungal community using molecular methods revealed putative species in tomato roots and soil. Functional information for identified species and genera can be obtained through culture-dependent, bioassay methods, and direct functional gene analysis. More comprehensive information about the soil and root fungal communities will provide a better understanding of the functional changes in the soil ecosystem due to the alterations in soil fungal communities by different agricultural practices. Future studies should concentrate on defining the ecological consequences of changes in the soil fungal community. Widely available culture-dependent methods augmented by PCR-based molecular methods for assessment of soil fungal biodiversity and community structure, and bioassay and functional gene assay methods for understanding of the functions of fungi in soil ecosystems should provide information on sustainable agricultural production systems and a basis for understanding the relationships between soil fungal biological and functional diversity.

Technical Abstract: Diversity and composition of soil and root colonizing fungi were examined in tomato (Lycopersicum esculentum = Solanum lycopersicum) plots subjected to diverse land and crop management systems. Culture-dependent colony counting was used to identify communities of fungi colonizing roots, and length heterogeneity polymerase chain reaction (LH-PCR) analysis of internal transcribed spacer-1 (ITS-1) profiles was used to characterize soil fungal communities. Diversity of soil fungi in bahiagrass (Paspalum notatum var. notatum ‘Argentine’) or undisturbed weed fallow plots was significantly lower when compared to diversity in organically managed plots. However, the diversity of root colonizing fungi was significantly lower in organic plots when compared to the bahiagrass or weed fallow plots. Multivariate analysis of root colonizing fungi and genetic ITS-1 profiles of soil fungi both indicated a higher degree of similarity among fungal communities in weed fallow and bahiagrass plots. Soil fungal communities in organically managed plots displayed a high degree of similarity to each other and were unique when compared to communities in other land management systems. A dominant 341-bp amplicon was identified in all soil fungal communities except those from organic plots. The amplicon was identified as Fusarium oxysporum by cloning and sequence analysis and confirmed by the LH-PCR amplicon size and sequences for a known F. oxysporum isolate. Fusarium oxysporum ominated all communities of root colonizing fungi except those subjected to organic management practices. This study addresses the benefits of integrating whole community analysis (soil fungi) with an approach targeting a functional subset (root colonizing fungi).