Discriminating the effects of agricultural land management practices on soil fungal communities

Authors: WU, TIEHANG - UNIVERSITY OF FLORIDA; Chellemi, Daniel; GRAHAM, JIM - UNIVERSITY OF FLORIDA; MARTIN, KENDALL - WILLIAM PATTERSON UNIV.; Rosskopf, Erin

Submitted to: Soil Biology and Biochemistry
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/21/2006
Publication Date: 1/12/2007
Citation: Wu, T., Chellemi, D.O., Graham, J., Martin, K., Rosskopf, E.N. 2007. Discriminating the effects of agricultural land management practices on soil fungal communities. Soil Biology and Biochemistry.

Interpretive Summary: Soil fungi play a critical role in regulating terrestrial ecosystems. In high-value crop production systems, plant pathogenic soil fungi have become an increasing concern due to the impending phase-out of the soil fumigant methyl bromide. Considerable research effort has been focused on the short-term goal of identifying alternative chemical fumigants for soil disinfestation. However, this approach does not address the root cause for epidemics of plant diseases caused by soil fungi and negates the contribution of soil fungi to the regulation of soil ecosystems. Agricultural land management practices can greatly influence outbreaks of plant disease caused by soilborne fungi. Organic soil amendments, tillage practices and rotational crops have all been used by farmers to reduce the incidence of plant disease caused by soil fungi. While their effects on populations of the plant pathogen have been adequately described, information regarding their impacts on soil fungal communities is paramount to the creation of crop production systems that minimize disruption to the agroecosystem in addition to mitigating pest outbreaks. The objective of this study was to identify the impacts of agricultural land management practices on the structure of soil fungal communities. This was accomplished by delineating and statistically discriminating soil fungal communities under five diverse land management treatments and the subsequent production of fresh market tomatoes. This study focused on land management and crop production practices that offer non-chemical alternatives to soil fumigation with methyl bromide for the management of soilborne pests of fresh market tomato and is part of a larger, multidispinary effort to develop efficient, economically feasible fresh market vegetable production systems that minimize disruption of the environment. Three years after initiation of land management practices, univariate analysis of genetic diversity failed to detect differences among soil fungal communities in plots managed organically, conventionally or maintained free of vegetation by continuous tillage (disk fallow). Genetic diversity was signific. Diversity of soil fungal communities was significantly reduced following the cultivation of tomato in year four when compared to the diversity in plots where tomato was not cultivated. Divergence in the composition of soil fungal communities was observed following the cultivation of tomato under all land management regimes except organic, where communities continued to remained clustered based upon similarities among their ITS-1 amplicons. Divergence in the composition of fungal communities became more pronounced following two major hurricanes (Francis and Jeanne, September, 2004) except for communities in the organic and pasture grass plots. Following the completion of a second tomato crop in year 5, genetic diversity and richness was similar under all land management regimes except the pasture grass, where it remained significantly higher. By contrast, unique by mutually similar compositions of fungal communities were only detected in plots under the organic land management regime following two consecutive years of tomato production. This was supported by observations that fungal communities were dominated by a 341bp rDNA amplicon fragment closely related to Fusarium oxysporumin all land management regimes except the organic. Thus, land management practices disturbing or disrupting soil fungal communities will significantly reduce their diversity. However, the composition of soil fungal communities is more strongly influenced by the type of land management practice and communities within an organically management system can be resistant to anthropogenic and meteorological disturbance events.

Technical Abstract: The structure of fungal communities was examined in soil subjected to five years of different agricultural land management and tomato production practices. Length heterogeneity polymerase chain reaction (LH-PCR) of fungal rDNA internal transcribed spacer-1 (ITS-1) regions was used to create genomic fingerprints of the soil fungal communities. Three years after initiation of land management practices, univariate analysis of genetic diversity failed to detect differences among soil fungal communities in plots managed organically, conventionally or maintained free of vegetation by continuous tillage (disk fallow). Genetic diversity was significantly higher in plots maintained as a perennial pasture grass (Paspalum notatum var Argentine bahiagrass) or as an undisturbed weed fallow. Soil fungal communities within organic, pasture grass or disk fallow plots were separated into unique clusters by nonparametric multivariate analysis of their Bray-Curtis similarity matrices, computed from the relative abundance of ITS-1 amplicons, while communities within disk fallow and conventional plots could not be distinguished from each other. Diversity of soil fungal communities was significantly reduced following the cultivation of tomato in year four when compared to the diversity in plots where tomato was not cultivated. Divergence in the composition of soil fungal communities was observed following the cultivation of tomato under all land management regimes except organic, where communities continued to remained clustered based upon similarities among their ITS-1 amplicons. Divergence in the composition of fungal communities became more pronounced following two major hurricanes (Francis and Jeanne, September, 2004) except for communities in the organic and pasture grass plots. Following the completion of a second tomato crop in year 5, genetic diversity and richness was similar under all land management regimes except the pasture grass, where it remained significantly higher. By contrast, unique by mutually similar compositions of fungal communities were only detected in plots under the organic land management regime following two consecutive years of tomato production. This was supported by observations that fungal communities were dominated by a 341bp rDNA amplicon fragment in all land management regimes except the organic. Cloning and sequencing indicated that the 341 bp fragment by LH-PCR had a sequencing size of 343bp, which was closely related to Fusarium oxysporum. Thus, land management practices disturbing or disrupting soil fungal communities will significantly reduce their diversity. However, the composition of soil fungal communities is more strongly influenced by the type of land management practice and communities within an organically management system can be resistant to anthropogenic and meteorological disturbance events.