NOAA 'Omics Seminar Series (September 21, 2022): Metabarcoding to understand microbes on sugar kelp

This seminar is part of the NOAA 'Omics Seminar Series, which (generally) takes place on the third Wednesday of every month at 12pm ET / 9am PT. 'Omics describes a suite of cutting-edge tools used to analyze DNA, RNA, proteins, or metabolites.
Date: September 21, 2022
Title: Using metabarcoding to understand microbial communities on aquacultured sugar kelp - identifying the good and the bad players
Presenter: Dr. Yuan Liu
Abstract: Sugar kelp cultivation at the southern end of its range on the east coast of North America is being pursued commercially for human consumption, which demands a high-quality product. Blade quality can be compromised by attached organisms - epibionts. Biweekly examination of epibionts on sugar kelp was conducted April-May 2018, on a kelp farm in eastern Long Island Sound, CT, USA. Culturable Vibrio spp. were not present on kelp blades until May and were limited to only old sections. No Vibrio colonies were human pathogens V. parahaemolyticus or V. vulnificus, based upon ToxR-specific multiplex PCR assays. Neither epibenthic cyanobacteria Lyngbya spp. nor the dinoflagellate Prorocentrum lima, microbes of concern because of toxigenicity, were detected on kelp by microscopy or metabarcoding of partial rRNA genes. Summarizing most-common sequence reads, Gammaproteobacteria was the most abundant bacterial group on kelp blades (49%) and Alphaproteobacteria were the most abundant in seawater (39%). Bacillariophyta were the most abundant eukaryotes on kelp blades (36%) and Dinoflagellata were the most abundant eukaryotes in seawater (43%). Molecular operational taxonomic unit matrices were used for non-metric multidimensional scaling; the most prominent structure for both prokaryotic and eukaryotic communities was the separation between blade and seawater samples. Indicator Species Analysis identified Gammaproteobacteria (55%) and Bacillariophyta (56%) to be the most important blade indicator prokaryotes and eukaryotes, respectively. A closer examination of indicator species temporal patterns and their ecophysiology suggested that Aquimarina, Parcubacteria, and Peronosporomycetes are potential pathogens to sugar kelp. Ciliates may be the most important grazers that keep epiphytes (Bacillariophyta, Rhodophyta, and Phaeophyta) and Peronosporomycetes on kelp in check.