Normal Operating Range of Bacterial Communities in Soil Used for Potato Cropping

Abstract

bIn this study, the impacts of six potato (Solanum tuberosum) cultivars with different tuber starch allocations (including one genetically modified [GM] line) on the bacterial communities in field soil were investigated across two growth seasons interspersed with 1 year of barley cultivation, using quantitative PCR, clone library, and PCR-denaturing gradient gel electrophoresis (DGGE) analyses. It was hypothesized that the modifications in the tuber starch contents of these plants, yielding changed root growth rates and exudation patterns, might have elicited altered bacterial communities in the soil. The data showed that bacterial abundances in the bulk soil varied over about 2 orders of magnitude across the 3 years. As expected, across all cultivars, positive potato rhizosphere effects on bacterial abundances were noted in the two potato years. The bulk soil bacterial community structures revealed progressive shifts across time, and moving-window analysis revealed a 60% change over the total experiment. Consistent with previous findings, the community structures in the potato rhizosphere compartments were mainly affected by the growth stage of the plants and, to a lesser extent, by plant cultivar type. The data from the soil under the non-GM potato lines were then taken to define the normal operating range (NOR) of the microbiota under potatoes. Interestingly, the bacterial communities under the GM potato line remained within this NOR. In regard to the bacterial community compositions, particular bacterial species in the soil appeared to be specific to (i) the plant species under investigation (barley versus potato) or, with respect to potatoes, (ii) the plant growth stage. Members of the genera Arthrobacter, Streptomyces, Rhodanobacter, and Dokdonella were consistently found only at the flowering potato plants in both seasons, whereas Rhodoplanes and Sporosarcina were observed only in the soil planted to barley.

The rhizosphere revisited: root microbiomics

“…Also within a specific bacterial group like fluorescent Pseudomonas spp., plant species-specific rhizosphere populations could be isolated (Glandorf et al, 1993; Lemanceau et al, 1995). More recent studies, in which the rhizosphere microbiomes were characterized based on direct extraction of total community DNA, also provide strong evidence for plant species-specific microbiomes (Miethling et al, 2000; Smalla et al, 2001; Kirk et al, 2005; Inceoglu et al, 2013). The roots of wheat, maize, rape, and barrel clover were shown to carry different bacterial communities as a consequence of assimilation of root exudates (Haichar et al, 2008).…”

“…The roots of wheat, maize, rape, and barrel clover were shown to carry different bacterial communities as a consequence of assimilation of root exudates (Haichar et al, 2008). Bacterial community structures in field grown potato rhizospheres were affected by the growth stage of the plant (Inceoglu et al, 2013). Also at the genotype level within a plant species, specificity of the rhizosphere microbiome has been described (Micallef et al, 2009a, b; Weinert et al, 2011).…”

Biotic Interactions in the Rhizosphere: A Diverse Cooperative Enterprise for Plant Productivity

“…It is known that different types of plants (Haichar et al, 2008) or even different ages of a plant İnceo glu et al, 2013) can harbor totally different microbial communities. A recent work argues that Arabidopsis is a limited model for investigating the impact of stress on rhizosphere community composition and function (Blee et al, 2013).…”

Microbiomics: An Approach to Community Microbiology

“…Further, plant species-specifi c rhizosphere populations could be isolated within a specifi c bacterial group such as fl uorescent Pseudomonas spp., . More recent studies, in which the rhizosphere microbiomes were characterized based on direct extraction of total community DNA, also provide strong evidence for plant species-specifi c microbiomes (Kirk et al 2005 ;Inceoglu et al 2013 ). The roots of wheat, maize, rape, and barrel clover were shown to carry different bacterial communities as a consequence of assimilation of root exudates (Haichar et al 2008 ).…”

“…The roots of wheat, maize, rape, and barrel clover were shown to carry different bacterial communities as a consequence of assimilation of root exudates (Haichar et al 2008 ). Bacterial community structures in fi eldgrown potato rhizospheres were affected by the growth stage of the plant (Inceoglu et al 2013 ). Further, at the genotype level within a plant species, specifi city of the rhizosphere microbiome has been described (Weinert et al 2011 ).…”