Browsing by Subject "community structure"
Now showing 1 - 2 of 2
Results Per Page
Sort Options
Item Discovering Ecological and Evolutionary Principles Governing Microbial Community Responses to Bacteriophage Infection of a Cross-Feeding Synthetic Coculture and Implications for Phage-based Applications(2020-08) Fazzino, LisaBacterial viruses, called bacteriophage (phage), infect bacteria and alter microbial community structure. Phages are an untapped resource to manipulate agriculture and medically applicable microbial communities. Yet, we cannot predict how phage impact a microbial community. My research aims to uncover ecological and evolutionary principles governing responses of microbial communities that contain cross-feeding interactions, where one species provides nutrients to (‘feeds’) another, phage. I combine wet-lab experiments on an engineered microbial co-culture with mathematical modeling to explore aspects of phage infection that are difficult to manipulate experimentally. I use a cross-feeding bacterial co-culture with Escherichia coli (E. coli) and Salmonella enterica (S. enterica) bacterial strains. In this cross-feeding system, E. coli cannot produce methionine, but does produce acetate and galactose. E. coli is paired with S. enterica that over-produces methionine and consumes acetate and galactose that E. coli secretes. To this co-culture, I add phage that infect either species. I have asked how simple cross-feeding co-cultures respond to phage infection. In Chapter 2, I used mathematical modeling and wet-lab experiments to show that single phage infections can break the cross-feeding relationship by liberating nutrients previously sequestered in the infected bacterial cells, ultimately changing community composition, and that partial, not full, resistance was necessary for this effect. In Chapter 3, ‘cocktails’ made of two different phage suppressed community growth the longest in a novel formulation that targeted both the pathogenic bacterial species and the slowest growing cross-feeder. Mathematical modeling showed that this was a generalizable concept to all cross-feeding systems. In Chapter 4, despite impacting community structure, I found that long term co-evolution between phage and E. coli cross-feeding with S. enterica only had weak effects on rates of adaptation. Phage treatments tended to increase rates of adaptations, as predicted by the Red Queen hypothesis, and cross-feeding tended to decrease rates of adaptation, as predicted by the Red King hypothesis. Overall, this thesis helps set baseline expectations of how phage influence cross-feeding microbial communities.Item The diversity and co-occurrence patterns of N2-fixing communities in a CO2-enriched grassland ecosystem(springer, 2016) Tu, Qichao; Zhou, Xishu; He, Zhili; Xue, Kai; Wu, Liyou; Reich, Peter B; Hobbie, Sarah; Zhou, JizhongDiazotrophs are the major organismal group responsible for atmospheric nitrogen (N2) fixation in natural ecosystems. The extensive diversity and structure of N2-fixing communities in grassland ecosystems and their responses to increasing atmospheric CO2 remain to be further explored. Through pyrosequencing of nifH gene amplicons and extraction of nifH genes from shotgun metagenomes, coupled with co-occurrence ecological network analysis approaches, we comprehensively analyzed the diazotrophic community in a grassland ecosystem exposed to elevated CO2 (eCO2) for 12 years. Long-term eCO2 increased the abundance of nifH genes but did not change the overall nifH diversity and diazotrophic community structure. Taxonomic and phylogenetic analysis of amplified nifH sequences suggested a high diversity of nifH genes in the soil ecosystem, the majority belonging to nifH clusters I and II. Co-occurrence ecological network analysis identified different co-occurrence patterns for different groups of diazotrophs, such as Azospirillum/Actinobacteria, Mesorhizobium/Conexibacter, and Bradyrhizobium/Acidobacteria. This indicated a potential attraction of non-N2-fixers by diazotrophs in the soil ecosystem. Interestingly, more complex co-occurrence patterns were found for free-living diazotrophs than commonly known symbiotic diazotrophs, which is consistent with the physical isolation nature of symbiotic diazotrophs from the environment by root nodules. The study provides novel insights into our understanding of the microbial ecology of soil diazotrophs in natural ecosystems.