UC Berkeley

This dissertation explores symbiotic microbial community ecology. Symbiosis is a prominent, and yet relatively under-studied phenomenon between two or more organisms. The scope of symbiosis is wide ranging, occurring between macro-macro organisms, micro-micro organisms, macro-micro organisms and everything in between. The span of symbiosis is great, from parasitic to mutually beneficial relationships between the organisms involved. The three chapters presented here comprise an initial look into symbiotic ecosystems using cutting edge sequencing technology. The studies aimed to discover interactions between bacterial microbes and their eukaryotic partners.

Chapter 1 describes the microbes that live in the gut of the passalid beetle, Odontotaenius disjuctus. This beetle feeds only on wood, which is low in nutrients, particularly nitrogen. Parallel to the termite-microbe system, I hypothesized that these microbes assist the beetles in digestion of the wood. PhyloChip microarray technology was used to characterize the microbial communities. I found that each gut region (there are 4) of the beetle contained a different microbial community, and that the anterior hindgut of the beetle contained strong anaerobic signals whereas other parts of the gut were more aerobic. The microbes that live in each of these gut regions reflect the oxygen availability of that environment. There was also a signal of potential nitrogen fixation in the anaerobic anterior hindgut.

In chapter 2 and 3, I explored fungal-bacterial interactions. Fungal-bacterial interactions have been sparsely characterized, appearing sporadically in the literature. Some studies describe bacteria found on the outside of the fungal hyphae, other times on the inside. One remarkable study found that a pathogenic fungus was not pathogenic without its toxin-producing endosymbiont. Other studies focused on the interaction between leaf-cutting ants, fungi, and bacteria associates. Of the estimated 1.5 million species of fungi, this interaction must be tremendously widespread and waiting to be characterized.

In chapter 2, I explored the microbial communities that live with various ectomycorrhizal fungi. Mycorrhizal fungi exchange mineral nutrients with plants for photosynthetic carbon. The experiments were designed to test for species and/or community specificity of bacteria to their fungal hosts. Several studies have aimed to answer similar questions, but the difference between the experiments presented in this chapter and others is that this involved temporal component, many more samples, and 454 sequencing that produced many orders of magnitude more sequences. The results showed that fungal species strongly determines the bacterial community. Burkholderia and members of the Rhizobiales were the most commonly encountered bacteria. Some of these have been found by other researchers, indicating a tight relationship between them.

And finally, in chapter three, I explored the interactions between saprobic fungi that form fungal mats in the soil and the bacteria that live with them. I tested for differences in bacterial community between fungal mat and non-mat leaf litter, whether fungal species has an influence on the bacterial community, and whether any distinct taxonomic group of bacteria were associated with the fungi. 454 pyrosequencing technology was employed for this purpose. The results showed that there is a strong difference in bacterial community composition between mat and non-mat litter. The Actinobacteria, particularly a Pseudonocardia species, showed strong preference for fungal mats. Pseudonocardia species are known for their antibiotic production and have been reported growing with other organisms, the most famous being the interactions between leaf-cutting ants, fungi, and Pseudonocardia.

Together, these three chapters provide different windows in which to peer into the world of microbial symbiosis, particularly those of bacteria with animal, plants, and fungi. It can be concluded that different symbiotic environments will select for different communities of bacteria, such as different gut sections and the presence of different species of fungi. When high throughput sequences of these environments are examined carefully, they can reveal clues into the important organisms that persist and participate in the ecology of said environments, priming for more extensive studies in symbiosis.