Elucidation of the bacterial communities associated with the harmful microalgaeAlexandrium tamarenseandCochlodinium polykrikoidesusing nanopore sequencing

Hyeonseok Shin,Suhyung Cho,So-Ra Ko,Hee-Mock Oh,Jongoh Shin,Hyung-Seok Oh,Byung-Kwan Cho,Eunju Lee,Chi-Yong Ahn

doi:10.1038/s41598-018-23634-6

Abstract

Interactions between microalgae and bacteria are often obligatory for harmful algal blooms (HABs). Here, we investigated the specific bacterial communities associated with Alexandrium tamarense and Cochlodinium polykrikoides, which cause ecological and economic damage during their blooms. To this end, the bacterial metagenome was selectively isolated from the two dinoflagellates and subsequently used for 16S rRNA analysis via the Nanopore MinION and Illumina sequencing platforms. Although the full-length 16S rRNA reads from the MinION platform showed high correlation in higher taxonomic ranks to the partial-length 16S rRNA reads from the Illumina platform, there was less correlation at the genus and species levels. MinION reads that are similar in the V3-V4 hypervariable regions with Illumina reads are classified to different taxonomies due to the extra information encoded in the full-length 16S rRNA reads. This indicates that bias arising from the short length Illumina reads can be supplemented by MinION reads. Furthermore, integrated analysis of the Illumina and MinION data showed that A. tamarense was predominantly enriched in the Roseobacter clade and C. polykrikoides was enriched in Gammaproteobacteria and Alphaproteobacteria. These results suggest that the association of different bacterial communities with A. tamarense and C. polykrikoides may be required for HABs.

Highlights

Harmful algal blooms (HABs) are annually recurring phenomena that cause environmental and economic damage to marine environments and industries worldwide[1,2,3,4]
To identify the bacteria associated with microalgae, we pre-cultivated A. tamarense and C. polykrikoides in laboratory conditions of sterile F/2 media, 100 μmolE m−2 s−1 light intensity, and 20 °C with an alternating 12 h light and dark cycle
The bacterial cells associated with A. tamarense and C. polykrikoides were isolated by selective disruption of the eukaryotic microalgae, while the bacterial cells remained mostly intact (Fig. 1A)

Summary

Results and Discussion

To determine whether the bacterial communities identified by Illumina and MinION data correlate, we compared the relative abundance and phylogenetic distance between samples using the merged OTU table, where rare species

Methods

Author Contributions

Additional Information