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Biotic stress shifted structure and abundance of Enterobacteriaceae in the lettuce microbiome.

Erlacher A, Cardinale M, Grube M, Berg G - PLoS ONE (2015)

Bottom Line: Both stress factors shifted the bacterial community of the leaf habitat, characterized by increases of species abundance and diversity.For the rhizosphere, we observed significant structural shifts of Enterobacteriaceae communities but also a high degree of resilience.The observed presence influenced by stress factors and the endophytic life style of Enterobacteriaceae on lettuce can be an important aspect in relation to human health.

View Article: PubMed Central - PubMed

Affiliation: Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria; Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010, Graz, Austria.

ABSTRACT
Lettuce cultivars are not only amongst the most popular vegetables eaten raw, they are also involved in severe pathogen outbreaks world-wide. While outbreaks caused by Enterobacteriaceae species are well-studied, less is known about their occurrence in natural environments as well as the impact of biotic stress. Here, we studied the ecology of the human health-relevant bacterial family Enterobacteriaceae and assessed the impact of biotic disturbances by a soil-borne phytopathogenic fungus and Gastropoda on their structure and abundance in mesocosm and pot experiments. Using a polyphasic approach including network analyses of 16S rRNA gene amplicon libraries, quantitative PCR and complementary fluorescence in situ hybridization (FISH) microscopy we found substantial yet divergent Enterobacteriaceae communities. A similar spectrum of 14 genera was identified from rhizo- and phyllospheres but the abundance of Enterobacteriaceae was on average 3fold higher in phyllosphere samples. Both stress factors shifted the bacterial community of the leaf habitat, characterized by increases of species abundance and diversity. For the rhizosphere, we observed significant structural shifts of Enterobacteriaceae communities but also a high degree of resilience. These results could be confirmed by FISH microscopy but it was difficult to visualize phyllosphere communities. Additional inoculation experiments with Escherichia coli as model revealed their presence below the wax layer as well as in the endosphere of leaves. The observed presence influenced by stress factors and the endophytic life style of Enterobacteriaceae on lettuce can be an important aspect in relation to human health.

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Related in: MedlinePlus

Taxonomic classification and relative abundance of Enterobacteriaceae associated with L. sativa var. capitata of phyllo- and rhizosphere samples.Genera below 1% abundance in any sample were shaded in grey (taxon legend). (Treatments; C = Control/untreated, G = Gastropoda, RS = R. solani; time of samplings T0–T3; P1–3 phyllosphere (replicates), R1–3 rhizosphere (replicates))
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pone.0118068.g001: Taxonomic classification and relative abundance of Enterobacteriaceae associated with L. sativa var. capitata of phyllo- and rhizosphere samples.Genera below 1% abundance in any sample were shaded in grey (taxon legend). (Treatments; C = Control/untreated, G = Gastropoda, RS = R. solani; time of samplings T0–T3; P1–3 phyllosphere (replicates), R1–3 rhizosphere (replicates))

Mentions: Altogether, 454 pyrosequencing of 16S rRNA gene amplicons revealed 14 distinct enterobacterial genera in the rhizosphere and phyllosphere of pot- and mesocosm-grown lettuce plants (Fig. 1). The enterobacterial microbiome contained taxa belonging to Escherichia/Shigella, Pantoea, Enterobacter and Enterobacteriaceae not classified at the genus level. Although these were identified as the most abundant taxa across the whole dataset, Escherichia/Shigella was only allocated to the mesocosm samples and was absent in the pot-grown samples. In contrast, we found Pantoea only in samples associated to the pot-grown plants from the first experiment. Enterobacter was the only identified taxa found in every sample and represents a core taxon. A comparison between the rhizosphere and the phyllosphere revealed that there were no significant structural differences, however the abundance of Enterobacteriaceae was statistically significantly higher (p<0.05) in a 3:1 ratio on phyllosphere samples determined with quantitative PCR. Interestingly, the occurrence of Yersinia was related to an absence of Pantoea in the rhizosphere.


Biotic stress shifted structure and abundance of Enterobacteriaceae in the lettuce microbiome.

Erlacher A, Cardinale M, Grube M, Berg G - PLoS ONE (2015)

Taxonomic classification and relative abundance of Enterobacteriaceae associated with L. sativa var. capitata of phyllo- and rhizosphere samples.Genera below 1% abundance in any sample were shaded in grey (taxon legend). (Treatments; C = Control/untreated, G = Gastropoda, RS = R. solani; time of samplings T0–T3; P1–3 phyllosphere (replicates), R1–3 rhizosphere (replicates))
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4340628&req=5

pone.0118068.g001: Taxonomic classification and relative abundance of Enterobacteriaceae associated with L. sativa var. capitata of phyllo- and rhizosphere samples.Genera below 1% abundance in any sample were shaded in grey (taxon legend). (Treatments; C = Control/untreated, G = Gastropoda, RS = R. solani; time of samplings T0–T3; P1–3 phyllosphere (replicates), R1–3 rhizosphere (replicates))
Mentions: Altogether, 454 pyrosequencing of 16S rRNA gene amplicons revealed 14 distinct enterobacterial genera in the rhizosphere and phyllosphere of pot- and mesocosm-grown lettuce plants (Fig. 1). The enterobacterial microbiome contained taxa belonging to Escherichia/Shigella, Pantoea, Enterobacter and Enterobacteriaceae not classified at the genus level. Although these were identified as the most abundant taxa across the whole dataset, Escherichia/Shigella was only allocated to the mesocosm samples and was absent in the pot-grown samples. In contrast, we found Pantoea only in samples associated to the pot-grown plants from the first experiment. Enterobacter was the only identified taxa found in every sample and represents a core taxon. A comparison between the rhizosphere and the phyllosphere revealed that there were no significant structural differences, however the abundance of Enterobacteriaceae was statistically significantly higher (p<0.05) in a 3:1 ratio on phyllosphere samples determined with quantitative PCR. Interestingly, the occurrence of Yersinia was related to an absence of Pantoea in the rhizosphere.

Bottom Line: Both stress factors shifted the bacterial community of the leaf habitat, characterized by increases of species abundance and diversity.For the rhizosphere, we observed significant structural shifts of Enterobacteriaceae communities but also a high degree of resilience.The observed presence influenced by stress factors and the endophytic life style of Enterobacteriaceae on lettuce can be an important aspect in relation to human health.

View Article: PubMed Central - PubMed

Affiliation: Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria; Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010, Graz, Austria.

ABSTRACT
Lettuce cultivars are not only amongst the most popular vegetables eaten raw, they are also involved in severe pathogen outbreaks world-wide. While outbreaks caused by Enterobacteriaceae species are well-studied, less is known about their occurrence in natural environments as well as the impact of biotic stress. Here, we studied the ecology of the human health-relevant bacterial family Enterobacteriaceae and assessed the impact of biotic disturbances by a soil-borne phytopathogenic fungus and Gastropoda on their structure and abundance in mesocosm and pot experiments. Using a polyphasic approach including network analyses of 16S rRNA gene amplicon libraries, quantitative PCR and complementary fluorescence in situ hybridization (FISH) microscopy we found substantial yet divergent Enterobacteriaceae communities. A similar spectrum of 14 genera was identified from rhizo- and phyllospheres but the abundance of Enterobacteriaceae was on average 3fold higher in phyllosphere samples. Both stress factors shifted the bacterial community of the leaf habitat, characterized by increases of species abundance and diversity. For the rhizosphere, we observed significant structural shifts of Enterobacteriaceae communities but also a high degree of resilience. These results could be confirmed by FISH microscopy but it was difficult to visualize phyllosphere communities. Additional inoculation experiments with Escherichia coli as model revealed their presence below the wax layer as well as in the endosphere of leaves. The observed presence influenced by stress factors and the endophytic life style of Enterobacteriaceae on lettuce can be an important aspect in relation to human health.

Show MeSH
Related in: MedlinePlus