Submitted to: Microbial Ecology
Publication Type: Peer reviewed journal
Publication Acceptance Date: 5/2/2007
Publication Date: 7/7/2007
Citation: Wu, T., Chellemi, D.O., Graham, J., Martin, K., Rosskopf, E.N. 2007. Comparison of soil bacterial communities under diverse agricultural land management and crop production practices. Microbial Ecology. Interpretive Summary: Bacteria are the most abundant and diverse group of organisms in soil with estimates of 104 – 106 distinct genomes per gram of soil. They are critical to many of the biological, chemical and physical processes that drive terrestrial ecosystems. Plant growth is affected directly through their activities as plant pathogens or plant growth promoters and indirectly via interactions with other soil microorganisms. Several key inorganic nutrients (C, N S, Fe, Ni and Ag etc.) in soil are transformed and cycled through their metabolic activities. Soil structure is affected through their production of organic and inorganic acids, facilitating the weathering of soil minerals and formation of soil aggregates. By virtue of their varied contributions to soil ecosystem function, bacteria are pivotal in the production of food and fiber from agricultural cropping systems. Thus, efforts to develop more sustainable systems that seek to minimize environmental disruption while maintaining plant health are contingent upon defining the impacts of land management and crop production practices on the structure and composition of soil bacterial communities. The objective of this study was to identify the impacts of agricultural land management and crop production practices on the structure and composition of soil bacterial communities in a humid, subtropical region. A culture-independent microbial community fingerprinting method (LH-PCR) was combined with univariate and multivariate analysis to statistically discriminate soil bacterial communities under five diverse land management treatments prior to and following the initiation of tomato crop production practices. Experiment conducted in large 0.16 ha replicated field plots managed under commercial production practices over a five-year period. This study focused on land management and crop production practices that provide chemical and nonchemical alternatives to soil fumigation with methyl bromide for the management of soilborne pests of fresh market tomato. It is part of a larger, multidispinary effort to develop economically-feasible fresh market vegetable production systems that minimize environmental disruption. Agricultural land management practices engaged over a 3-4 year period, significantly impacted the structure of soil bacterial communities, as revealed in the July samples. Diversity, indicated by the Shannon-Weiner index (H'), was higher in the organically managed system when compared to the perennial pasture grass, undisturbed (weed fallow) and vegetation free (disk fallow) systems. However, comparisons between samples from the organic and conventionally managed systems revealed no significant differences in H'. A significant shift in the structure of soil bacterial communities was associated with the cultivation of tomato
Technical Abstract: The composition and structure of bacterial communities was examined in soil subjected to a range of diverse agricultural land management and crop production practices. Length heterogeneity polymerase chain reaction (LH-PCR) of bacterial DNA extracted from soil was used to generate amplicon profiles that were analyzed with univariate and multivariate statistical methods. Land management treatments were initiated in June 2000. In soil sampled July 2003, the diversity of bacterial 16S rDNA amplicons was higher in undisturbed plots (weed fallow), plots subjected to organic production standards and plots maintained under conventional tomato production practices than in plots maintained free of vegetation (disk fallow) or planted to a perennial pasture grass (Paspalum notatum var Argentine bahiagrass). In July 2004, diversity was higher in the conventional, organic and disk fallow plots. Land management practices did not affect the number of different bacterial 16S rDNA amplicons detected (richness) but did affect how the relative abundance of individual amplicons was distributed (evenness). Following cultivation of a tomato crop (Lycopersicon esculentum) in 2003, diversity was higher in organic plots when compared to weed fallow and pasture grass plots but was not statistically different from diversity in conventional or disk fallow plots. Diversity was higher in soil subjected to repeated cultivation of tomato. In July 2003, the genetic composition of soil bacterial communities in the perennial pasture grass and weed fallow plots were similar to each other and distinct from other bacterial communities. Following cultivation of tomato, soil bacterial communities in perennial pasture grass and weed fallow plots were indistinguishable from communities in the disk fallow and conventional plots. The composition of bacterial communities within replicate plots of the organically managed system remained similar to each other and distinct from communities in other land management systems despite repeated cultivation to tomato and damage from two major hurricanes, providing evidence of their ability to resist to anthropogenic and natural disturbance.