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Identification and genomic characterization of four novel Rhodobacteracae strains from the Point Loma kelp forest
Dinsdale, Elizabeth ALipson, DavidEdwards, Robert
xi, 67 pages : illustrations (some color).
Microbes colonizing the surface of macroalgae positively influence the growth, development, and morphology of the macroalgae. In return, the kelp provides organic substances creating a nutrient-rich surface habitat for the settling microbial community. Metagenomic inquiries have identified the taxonomy of the microbial community associated with the Giant Kelp (Macrocystis pyrifera). However, there is a lack of understanding the functional interaction between the microbes and the M. pyrifera. My research will fill in those gaps of knowledge by using whole genome sequencing to identify the taxonomy and functions of four novel strains. Overall, the partnership of metagenomic and whole genome sequencing data can push the envelope to a better understanding of the micro-algae relationship. The four novel Rhodobacteraceae strains (ED522, ED523, ED524 and ED575) were isolated exclusively from the surface of M. pyrifera from Point Loma, San Diego and sequenced on the Ion Torrent Personal Genome Machine (PGM) platform. The genomic subsystem annotation was executed via Rapid Annotation Subsystem Technology (RAST). 16S rRNA suggests all strains are members of the Rhodobacteraceae family. ED522 and ED523 exhibited 99.0 % similarity to Sulfitobacter donghicola. ED524 and ED575 respectively displayed 100.0 % similarity to Ascidiaceihabitans donghaensis. Although four strains were identified with high confidence based on 16S, their subsystem analysis suggests novelty as each genome possesses unique functions and distinct genotypic profiles. Results from the genomic subsystem analysis identified several potential positive interactions between the microbes and the kelp suggesting a mutualistic relationship. For example, all four strains decompose urea, degrade leucine and contain gene transfer agents (GTA). ED524 and ED575 can utilize taurine (as a sulfur source), oxidize sulfur, contain a light harvesting (LH) and reaction center (RC) for photosynthesis and synthesize leucine. ED575 can degrade both valine and isoleucine. This study will provide a deeper understanding of the microbe-algae relationship of M. pyrifera living in Point Loma, San Diego.
Biology with a concentration in Ecology
San Diego State University
Master of Science (M.S.) San Diego State University, 2016
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