La gestion efficace des champignons mycorhiziens arbusculaires (CMA) est largement considérée comme une stratégie prometteuse pour le développement de l’agriculture durable et de conservation. Or, la culture conventionnelle de Brassicaceae non-mycorhiziennes, un groupe qui comprend plusieurs cultures d’une grande importance économique en Amérique du Nord, telles que le chou régulier (Brassica oleracea var. capitata) et le brocoli (Brassica oleracea var. italica), peut réduire la densité des CMA dans les agroécosystèmes. Dans le but de réduire l’impact négatif des cultures de brocoli et de chou sur l’abondance des CMA au champ, nous proposons de cultiver ces plants en compagnonnage persistant avec du trèfle blanc (Trifolium repens L.), une plante dépendant largement des CMA. Nous avons testé l’impact de la culture intercalaire de B. oleracea, sur (1) la colonisation des racines de Brassicaceae par les CMA et le rendement de ces cultures, et (2) la vitesse et l’intensité de colonisation d’une culture subséquente associée aux CMA, le maïs sucré, et son rendement. Dans cette étude, nous avons observé que les CMA pouvaient coloniser et former des vésicules dans les racines de cultures de B. oleracea, même lorsque cultivées sans culture mycorhizienne d’entre-rang, probablement via d’autres sources de carbone. Néanmoins, plus de brocolis étaient colonisés lorsqu’ils étaient cultivés dans les parcelles avec trèfle, mais ils étaient colonisés à une plus basse intensité. Comme escompté, l’adoption d’une culture de couverture intercalaire de trèfle persistant à travers les deux rotations a réduit le délai de colonisation de la culture de maïs et en a augmenté le rendement. / Efficient management of arbuscular mycorrhizal fungi (AMF) holds much potential in conservation and sustainable agriculture. Growing non-mycorrhizal Brassicaceae crops, including crops of great economic importance in North America such as regular cabbage (Brassica oleracea var. capitata) and broccoli (B. oleracea var. italica), has been associated with reduced AMF density in agroecosystem. In the hope of reducing the negative impact of broccoli and cabbage culture on AMF abundance in fields, we cultivated these crops alongside mycorrhizal white clover (Trifolium repens L.) in a persistent intercropping system. We tested the impact of B. oleracea intercropping on (1) AMF root colonization levels and crop yield, and on (2) the AMF colonization speed and level, as well as the yield of a following mycorrhiza-dependent crop rotation, sweet maize (Zea mays L.) In this study, we found that AMF could colonize and produce vesicles in B. oleracea crop roots, even when grown without a mycorrhizal intercrop, probably through other carbon sources. Intercropping with clover still led to more broccolis being colonized by AMF, but at a lower intensity than in sole crop plots. As expected, use of a persistent clover intercrop reduced colonization delay and increased yield of the subsequent maize rotation.

The vast majority of terrestrial plant species live in symbiosis with arbuscular mycorrhizal fungi (AMF). AMF and plants live in complex networks, with roots of individual plants hosting multiple AMF, and single AMF colonizing multiple plants concurrently. Through the exchange of resources, the two partners of this symbiosis can have great effects on each other, effects which can ripple through both communities. What determines the patterns of associations between the partners is still largely unknown. In this dissertation, I examine a variety of factors, and in particular host identity, that could drive the community composition of AMF in roots. I began by surveying the diversity of AMF in roots of 12 plant species at a remnant bunchgrass prairie in Oregon, U.S.A. (Chapter 2). To do that, I first designed new primers for use in polymerase chain reaction (PCR) to specifically amplify DNA from all Glomeromycota species. Using those primers, I found 36 distinct AMF phylogenetic groups, or operational taxonomic units (OTUs) in the roots from the prairie. The proportion of OTUs in the basal order Archaeosporales was greater than in many other environmental surveys. I also conducted an in silico analysis to predict how effectively previously published primers would detect the whole diversity of OTUs I detected. I then assayed AMF community composition in the roots of 50 plants from nine plant species (Chapter 3). To do that, I designed primers specific to 18 of the OTUs detected in the initial field survey and used them to test for the presence of each OTU in the roots individual plants. I used that data to test if AMF community composition in individual roots correlated with host identity, spatial distribution, or soil characteristics. I found host identity was associated with both the richness and the structure of root AMF communities, while spatial distribution and soil characteristics were not. Finally, I performed an experimental test of the effect of host identity and community context on AMF community assembly (Chapter 4). I grew plants from four native perennial plant species, including two common and two federally endangered plants, either individually or in a community of four plants (with one plant of each species). I analyzed the AMF community composition in the roots of all plants after 12 weeks of growth with exposure to a uniform mix of field soil as inoculum. I found that host species identity affected root AMF richness and community composition, and community context affected AMF richness. Only one of the endangered species was highly colonized by AMF, and I did not detect unique AMF communities associated with it. This dissertation provides information on the diversity of AMF at a remnant bunchgrass prairie, an ecosystem which has been the subject of very few studies of AMF. Although a complex mix of factors interact to determine AMF community composition in roots, this work provides strong evidence that host identity plays a major role in that process. / Graduation date: 2013