Symbiosis and microbial genomics

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Symbiosis and genome evolution *Our longterm aim is to understand the impacts of major changes like horizontal gene transfer and symbiosis on genome structure and function in microbial eukaryotes. Here, we extend our work on endosymbiosis to complex symbiotic associations between microbes in two environments that are rich in symbiotic interactions; the hindgut of wood-eating insects, and coral reefs. **A. Protist-Bacteria Associations in the Termite Hindgut*The hindguts of termites and the wood-eating cockroach Cryptocercus harbour a complex, host-specific community of anaerobic protists and bacteria, the composition of which is stable through time. Within this symbiotic community are also many symbioses between the microbes: 60% of hindgut bacteria live inside or on the surface of a protist. The functions of these associations are unknown, although nitrogen metabolism has been implicated in some. We will use single-cell genomics and transcriptomics to address the following questions:*1. What is the functional relationship of epibionts to host protists? Epibionts, or surface symbionts, are not as well-studied as endosymbionts, but are nonetheless common in anaerobic environments, where many protists are coated with a monolayer like a `filter' between it and its environment. To examine the functional relationship between epibionts and host, we will characterize epibiont genomes and host transcriptomes from four hosts with a single epibiont species: Barbulonympha, Urinympha, Devescovina, and Staurojeonina. We will create metabolic maps for the epibionts, and identify pathways absent from host transcriptomes to test whether nitrogen metabolism is a general feature of such associations. We will also compare epibiont and endosymbiont genomes to identify any features that may functionally distinguish them. *2. Do multiple symbionts partition essential metabolic pathways? In sap-feeding insect with multiple endosymbionts, essential metabolic pathways have been partitioned between symbionts. We will test the hypothesis that this also explains epibiotic systems with multiple symbionts by sequencing epibiont genomes and host transcriptomes from Streblomastix and Calonympha. Metabolic mapping will show whether complete pathways are encoded within individual epibiont genomes or distributed among them. The symbionts of Streblomastix are of additional interest since the oxymonad host is a different lineage than most termite protists, and it is also not demonstrably cellulolytic. **B. Coral-Protist Associations*Coral reefs are hotspot for biodiversity and symbiotic interactions, but almost nothing is known about reef microbial eukaryotes. To develop reefs as a system to study symbiotic interactions at the genomic level, we will establish baseline information and address two specific questions:*1. Does the diversity of coral reef protist communities follow similar trends as bacteria and viruses? The characteristics of bacterial and viral communities in coral reefs have been documented, but not protists. To establish a baseline for comparisons, we will carry out protist surveys for 3 reef systems, as well as thrombolites (calcified microbial mat communities), using deep sequence tagging of the same samples used to study bacteria and viruses. We will also focus specifically on a gradient of reef degradation - from protected pristine reefs to heavily fished reefs with massive coral death. For bacteria, abundance and prevalence of heterotrophs increase over this gradient, and we will test the hypothesis that protists follow the same trends by applying the same methodology. Variation in abundance and taxonomic diversity along the gradient will be analysed and lineages specifically associated with reef degradation will be identified.