Abstract
BackgroundIn this study, we assessed the actively metabolizing bacteria in the rhizosphere of potato using two potato cultivars, i.e. the genetically-modified (GM) cultivar Modena (having tubers with altered starch content) and the near-isogenic non-GM cultivar Karnico. To achieve our aims, we pulse-labelled plants at EC90 stage with 13C-CO2 and analysed their rhizosphere microbial communities 24 h, 5 and 12 days following the pulse. In the analyses, phospholipid fatty acid/stable isotope probing (PLFA-SIP) as well as RNA-SIP followed by reverse transcription and PCR-DGGE and clone library analysis, were used to determine the bacterial groups that actively respond to the root-released 13C labelled carbonaceous compounds.Methodology/Principal findingsThe PLFA-SIP data revealed major roles of bacteria in the uptake of root-released 13C carbon, which grossly increased with time. Gram-negative bacteria, including members of the genera Pseudomonas and Burkholderia, were strong accumulators of the 13C-labeled compounds at the two cultivars, whereas Gram-positive bacteria were lesser responders. PCR-DGGE analysis of cDNA produced from the two cultivar types showed that these had selected different bacterial, alpha- and betaproteobacterial communities at all time points. Moreover, an effect of time was observed, indicating dynamism in the structure of the active bacterial communities. PCR-DGGE as well as clone library analyses revealed that the main bacterial responders at cultivar Karnico were taxonomically affiliated with the genus Pseudomonas, next to Gluconacetobacter and Paracoccus. Cultivar Modena mainly attracted Burkholderia, next to Moraxella-like (Moraxellaceae family) and Sphingomonas types.Conclusions/SignificanceBased on the use of Pseudomonas and Burkholderia as proxies for differentially-selected bacterial genera, we conclude that the selective forces exerted by potato cultivar Modena on the active bacterial populations differed from those exerted by cultivar Karnico.
Highlights
The living soil is often grossly carbon-limited and this constraint poses severe restrictions to the growth of heterotrophic bacteria
In this study, using both Phospholipid Fatty Acid (PLFA)-Stable isotope probing (SIP) and RNA-SIP approaches, we examined the bacterial communities that effectively accumulate the 13C label in carbonaceous molecules that are released by the roots of two different potato cultivars, i.e. the ware potato Karnico and its GM derivative Modena, into the rhizosphere soil system
We assessed the impact of 13C-labelled carbonaceous compounds released into the rhizosphere on the local bacterial communities associated with two potato cultivars, i.e. the parental line Karnico and the GM derivative Modena, using stable isotope probing [14]
Summary
The living soil is often grossly carbon-limited and this constraint poses severe restrictions to the growth of heterotrophic bacteria. The rhizosphere of plants represents a hotspot in soil where organic carbonaceous compounds are released by the roots [1]. Plants act as selectors of particular soil bacteria into their rhizospheres, promoting root colonization by primary and even secondary responders to root-excreted compounds [3,4]. Cultivar Modena, derived from parental cultivar Karnico, produces tubers with altered starch content. We assessed the actively metabolizing bacteria in the rhizosphere of potato using two potato cultivars, i.e. the genetically-modified (GM) cultivar Modena (having tubers with altered starch content) and the nearisogenic non-GM cultivar Karnico. Phospholipid fatty acid/ stable isotope probing (PLFA-SIP) as well as RNA-SIP followed by reverse transcription and PCR-DGGE and clone library analysis, were used to determine the bacterial groups that actively respond to the root-released 13C labelled carbonaceous compounds
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