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Accueil du site → Doctorat → États-Unis → 2015 → IDENTIFICATION OF FINE SCALE RESPONSES IN MILLET ROOT-ZONE MICROBIOMES TO INTERCROPPING WITH WOODY SHRUBS IN THE SAHEL.

Ohio State University (2015)

IDENTIFICATION OF FINE SCALE RESPONSES IN MILLET ROOT-ZONE MICROBIOMES TO INTERCROPPING WITH WOODY SHRUBS IN THE SAHEL.

Debenport, Spencer James

Titre : IDENTIFICATION OF FINE SCALE RESPONSES IN MILLET ROOT-ZONE MICROBIOMES TO INTERCROPPING WITH WOODY SHRUBS IN THE SAHEL.

Auteur : Debenport, Spencer James

Université de soutenance : Ohio State University

Grade : Doctor of Philosophy (PhD) 2015

Résumé
Plant associated microbiomes can have significant influence on plant health and development in agricultural enrivonments. In the desert ecosystem of the Sahel region in sub-Saharan Africa, a woody shrub intercropping system has been shown to improve yields of millet (Pennisetum glaucum) and peanut (Arachis hypogaea). The two shrubs involved in this intercropping system (Guiera senegalensis and Piliostigma reticulatum) are found throughout this region and have the potential to be utilized by subsistence farmers. This work describes the effect of intercropping with these two native shrubs on root-zone microbiome composition in both the millet and shrub intercropping partners. Two long term study sites were sampled where blocks of millet grown alone and shrubmillet intercropping with application of shrub residue mulch were present. At both long term study sites, a significant increase in millet yield (P < 0.05) was observed. In the first study, the root-zone microbiome composition of millet grown within and outside of this intercropping system were compared using high throughput amplicon sequencing techniques. Across four independent transects at these two sites, operational taxonomic units (OTUs) belonging to the genera Chitinophaga, Aspergillus, Coniella, Epicoccum, Fusarium, Gibberella, Lasiodiplodia, Penicillium, and Phoma were consistently significantly enriched in the root zones of intercropped millet plants. These enrichments ranged from 30- to 1000-fold increases in abundance. The organisms containing those OTU marker sequences could potentially be involved in the improved crop yield observed. In the second study, root-zone microbiomes of millet and shrub plants in the intercropping system were compared. Despite the homogenizing effect of the shrub residue on the soil, sub-genus level variation was observed in the fungal community between plant species. OTUs within the genera Aspergillus, Cochliobolus, Epicoccum, Fusarium, Gibberella, Lasiodiplodia, Paecilomyces, Penicillium, and Phoma were enriched in millet plants when compared to shrubs. Interestingly, there was a large overlap (7 of 9 genera) which were also enriched in intercropped millet plants when compared to millet grown alone. Between 80 and 92% of all OTUs within those genera demonstrated some form of crop or plant species specific enrichment. This is evidence that a specific sub-genus level population of these genera is a good colonizer of millet. In a third study, a quantitative method to independently validate patterns observed in high throughput sequencing techniques was tested. Primers selective to specific clusters of millet enriched OTUs were designed and tested for their ability to amplify target DNA. A primer selective for those Chitinophaga OTUs enriched in intercropped millet samples was used to selectively amplify DNA of the target size. Quantitative PCR using this primer independently validated the pattern of significant enrichment observed in samples of intercropped millet compared to millet grown alone. Fold change differences in abundance of target DNA were similar between techniques, with the high throughput sequencing method showing slightly inflated differences. This work demonstrates the strength of high throughput amplicon sequencing techniques to identify fine scale variations in plant microbiomes associated with phenomena in the field.

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Page publiée le 22 janvier 2016, mise à jour le 31 août 2017