Phylogeny, plant species, and plant diversity influence carbon use phenotypes among Fusarium populations in the rhizosphere microbiome

Carbon use by microorganisms in the rhizosphere microbiome has been linked to plant pathogen suppression and increased mineralization of soil nutrients for plant uptake; however, factors that influence carbon use traits are poorly understood for most microbial groups. This work characterized the relationships of phylogeny, plant species, and plant diversity with carbon use among fungi in the genus Fusarium from rhizosphere soil. Eighty-four randomly collected Fusarium isolates were cultured from the rhizosphere of the perennial plants Lespedeza capitata and Andropogon gerardii, maintained as long-term monocultures or growing in 16-plant species polycultures. For each isolate, a portion of the RPB2 locus was sequenced for phylogenetic analyses and growth on 95 carbon substrates was measured using Biolog SF-P2 plates. Similarity in carbon use among isolates decreased with increasing genetic distance and there were differences in niche width (i.e., number of carbon substrates used) and growth on preferred substrates (i.e., mean growth on the five carbon substrates supporting the greatest growth) among isolates within two predominant phylogenetic clades. Carbon use also varied with plant species and the diversity of the surrounding plant community. Within each of the two predominant clades, niche width was greater among Fusarium isolates from the rhizosphere of L. capitata than A. gerardii. The correspondence of phylogeny with carbon use suggests changes in Fusarium community composition may lead to the differential use of carbon substrates in the rhizosphere, while the effects of plant species and diversity suggest variation in plants communities may also correspond to variation in carbon use by these fungi. In addition, the consistent effect of plant species on niche width within different clades provides evidence that the rhizosphere environment of the two plants selects for particular traits, rather than promoting the presence of clades with those traits. Overall, this research shows the dynamics of plant and fungal communities are likely to influence carbon use in the rhizosphere and consequently processes related to this phenotype, such as soil nutrient cycling and competition for carbon among soil microbes.