Gordon, B. R. 2015. The influence of long-term nitrogen fertilization on symbiosis and metabolism in the legume-rhizobium mutualsim. Thesis, University of Illinois at Urban-Champaign, Urbana Illinois.
Understanding how mutualisms evolve in response to a changing environment will be critical for predicting the long-term impacts of global changes, such as increased nitrogen (N) deposition. Bacterial mutualists in particular might evolve quickly, thanks to short generation times and the potential for independent evolution of plasmids through recombination and/or horizontal gene transfer (HGT). In a previous work using the legume/rhizobia mutualism, we demonstrated that long-term nitrogen fertilization caused the evolution of less-mutualistic rhizobia. Here, I used two approaches to investigate the influence of long-term nitrogen fertilization on symbiosis and metabolism in Rhizobium. First, I used 63 of our previously isolated rhizobium strains in comparative phylogenetic and quantitative genetic analyses to determine the degree to which variation in partner quality is attributable to phylogenetic relationships among strains versus recent genetic changes in response to N-fertilization. I found evidence of distinct evolutionary relationships between chromosomal and pSym genes, and broad similarity between pSym genes. We also find that nifD has a unique evolutionary history that explains much of the variation in partner quality, and our results implicate MoFe subunit interaction sites in the evolution of less-mutualistic rhizobia. Second, I determined metabolic fingerprints from our Rhizobium isolates and integrated them with data on symbiotic quality and previously determined phylogenies, revealing that N-fertilization significantly contributed to our observed variation in metabolic capacity. Despite a weak general relationship between metabolism and partner quality, importantly, there appear to be functionally significant relationships between certain C-substrates and partner quality.
These results provide insight into the evolution of less-cooperative rhizobia in response to long-term N-fertilization, which significantly contributed to observed variation in partner quality and metabolic capacity. Nonsynonymous substitutions in nifD appear to be major contributors to variation in partner quality. Metabolic profile generally correlates poorly with partner quality, as does individual metabolite utilization. However, there is a relationship between functional significance of certain C-substrates and partner quality.