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Soil and cultivar type shape the bacterial community in the potato rhizosphere.

İnceoğlu Ö, Falcão Salles J, van Elsas JD - Microb. Ecol. (2011)

Bottom Line: However, no genetically modified plant effect was observed.Utilization of some of the carbon and sulfur sources was specific per cultivar, and different microbial communities were found as defined by cultivar.Thus, both soil and cultivar type shaped the potato root-associated bacterial communities that were responsive to some of the substrates in phenotype arrays.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbial Ecology, Centre for Life Sciences, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.

ABSTRACT
The rhizospheres of five different potato cultivars (including a genetically modified cultivar) obtained from a loamy sand soil and two from a sandy peat soil, next to corresponding bulk soils, were studied with respect to their community structures and potential function. For the former analyses, we performed bacterial 16S ribosomal RNA gene-based PCR denaturing gradient gel electrophoresis (PCR-DGGE) on the basis of soil DNA; for the latter, we extracted microbial communities and subjected these to analyses in phenotype arrays (PM1, PM2, and PM4, Biolog), with a focus on the use of different carbon, sulfur and phosphorus sources. In addition, we performed bacterial PCR-DGGE on selected wells to assess the structures of these substrate-responsive communities. Effects of soil type, the rhizosphere, and cultivar on the microbial community structures were clearly observed. Soil type was the most determinative parameter shaping the functional communities, whereas the rhizosphere and cultivar type also exerted an influence. However, no genetically modified plant effect was observed. The effects were imminent based on general community analysis and also single-compound analysis. Utilization of some of the carbon and sulfur sources was specific per cultivar, and different microbial communities were found as defined by cultivar. Thus, both soil and cultivar type shaped the potato root-associated bacterial communities that were responsive to some of the substrates in phenotype arrays.

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Dendrogram representing the similarity of PCR-DGGE profiles generated with 16S rRNA gene based bacterial DGGE for B and V soil at senescence stage. B Buinen, A Aveka, Av Aventra, K Karnico, M Modena, D Désierée, V Valthermond, sn senescence, b bulk
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Fig1: Dendrogram representing the similarity of PCR-DGGE profiles generated with 16S rRNA gene based bacterial DGGE for B and V soil at senescence stage. B Buinen, A Aveka, Av Aventra, K Karnico, M Modena, D Désierée, V Valthermond, sn senescence, b bulk

Mentions: Analyses of all patterns (using UPGMA with Pearson correlation) revealed two major clusters, one encompassing the patterns derived from all B soil derived samples; the other one encompassing those from all V soil ones, next to three B soil samples. The bulk soil samples clustered together inside the V soil cluster. Per soil, the rhizosphere-derived patterns all grouped apart from the corresponding bulk soil ones, thus indicating clear effects of the plant roots on the structures of the local bacterial communities. The rhizosphere effects were more evident for the B than for the V soil. That the effect of soil type was indeed stronger than that of cultivar was also apparent from the fact that the same cultivars grown in B versus V soil yielded different patterns, which grouped them in clusters defined by soil rather than cultivar type (Fig. 1).Figure 1


Soil and cultivar type shape the bacterial community in the potato rhizosphere.

İnceoğlu Ö, Falcão Salles J, van Elsas JD - Microb. Ecol. (2011)

Dendrogram representing the similarity of PCR-DGGE profiles generated with 16S rRNA gene based bacterial DGGE for B and V soil at senescence stage. B Buinen, A Aveka, Av Aventra, K Karnico, M Modena, D Désierée, V Valthermond, sn senescence, b bulk
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3275741&req=5

Fig1: Dendrogram representing the similarity of PCR-DGGE profiles generated with 16S rRNA gene based bacterial DGGE for B and V soil at senescence stage. B Buinen, A Aveka, Av Aventra, K Karnico, M Modena, D Désierée, V Valthermond, sn senescence, b bulk
Mentions: Analyses of all patterns (using UPGMA with Pearson correlation) revealed two major clusters, one encompassing the patterns derived from all B soil derived samples; the other one encompassing those from all V soil ones, next to three B soil samples. The bulk soil samples clustered together inside the V soil cluster. Per soil, the rhizosphere-derived patterns all grouped apart from the corresponding bulk soil ones, thus indicating clear effects of the plant roots on the structures of the local bacterial communities. The rhizosphere effects were more evident for the B than for the V soil. That the effect of soil type was indeed stronger than that of cultivar was also apparent from the fact that the same cultivars grown in B versus V soil yielded different patterns, which grouped them in clusters defined by soil rather than cultivar type (Fig. 1).Figure 1

Bottom Line: However, no genetically modified plant effect was observed.Utilization of some of the carbon and sulfur sources was specific per cultivar, and different microbial communities were found as defined by cultivar.Thus, both soil and cultivar type shaped the potato root-associated bacterial communities that were responsive to some of the substrates in phenotype arrays.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbial Ecology, Centre for Life Sciences, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.

ABSTRACT
The rhizospheres of five different potato cultivars (including a genetically modified cultivar) obtained from a loamy sand soil and two from a sandy peat soil, next to corresponding bulk soils, were studied with respect to their community structures and potential function. For the former analyses, we performed bacterial 16S ribosomal RNA gene-based PCR denaturing gradient gel electrophoresis (PCR-DGGE) on the basis of soil DNA; for the latter, we extracted microbial communities and subjected these to analyses in phenotype arrays (PM1, PM2, and PM4, Biolog), with a focus on the use of different carbon, sulfur and phosphorus sources. In addition, we performed bacterial PCR-DGGE on selected wells to assess the structures of these substrate-responsive communities. Effects of soil type, the rhizosphere, and cultivar on the microbial community structures were clearly observed. Soil type was the most determinative parameter shaping the functional communities, whereas the rhizosphere and cultivar type also exerted an influence. However, no genetically modified plant effect was observed. The effects were imminent based on general community analysis and also single-compound analysis. Utilization of some of the carbon and sulfur sources was specific per cultivar, and different microbial communities were found as defined by cultivar. Thus, both soil and cultivar type shaped the potato root-associated bacterial communities that were responsive to some of the substrates in phenotype arrays.

Show MeSH