Elucidation of the bacterial communities associated with the harmful microalgae Alexandrium tamarense and Cochlodinium polykrikoides using nanopore sequencing

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.

Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution

“…A prime example is the MinION™ sequencer from Oxford Nanopore Technologies, which is capable of producing long sequences with no theoretical read length limit [9][10][11]. MinION™ sequencing targets the entire 16S rRNA gene, allowing the identification of bacteria with more accuracy and sensitivity [12,13].…”

Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon

“…Several studies targeting the full-length 16S rRNA gene have already been performed using nanopore sequencing to: i) characterize artificial and already characterized bacterial communities (mock community) [15–17]; ii) characterize complex microbiota samples, from mouse gut [18], wastewater [19], microalgae [20] and dog skin [21]; and iii) characterize the pathogenic agent in a clinical sample [22–24]. On the other hand, only two studies have been performed using the whole rrn operon to characterize mock communities [25] and complex natural communities [26].…”

Nanopore sequencing of microbial communities reveals the potential role of sea lice as a reservoir for fish pathogens

“…Regarding the study of microbiota, several studies have been dedicated to compare taxonomical analysis derived by this technology with Illumina sequencing, and have shown that error rate has been compensated with larger fragments, providing in some cases higher taxonomical resolution 26,27 . Although the error rate remains the main limitation to the expansion of this sequencing methodology, it has been successfully applied in several species and tissues, identifying the microbiota present in complex samples from terrestrial 28,29 and aquatic environment 23,30 . Notably, nanopore sequencing has been applied to understand the interactions of human diseases 31 , environmental samples obtained from glacier regions 23 , ocean water column 32 and to identify the bacterial community associated with harmful microalgae 30 , and these studies demonstrate the potential and applicability of nanopore sequencing for microorganism detection in all environments.This study aimed to characterize the microbiota community associated with the salmon's ectoparasite Caligus rogercresseyi obtained from different geographical regions, using third-generation sequencing technology based on nanopore sequencing of full 16S rRNA gene.…”