Protocols for Monitoring Harmful Algal Blooms for Sustainable Aquaculture and Coastal Fisheries in Chile

Abstract

Harmful algae blooms (HABs) cause acute effects on marine ecosystems due to their production of endogenous toxins or their enormous biomass, leading to significant impacts on local economies and public health. Although HAB monitoring has been intensively performed at spatiotemporal scales in coastal areas of the world over the last decades, procedures have not yet been standardized. HAB monitoring procedures are complicated and consist of many methodologies, including physical, chemical, and biological water sample measurements. Each monitoring program currently uses different combinations of methodologies depending on site specific purposes, and many prior programs refer to the procedures in quotations. HAB monitoring programs in Chile have adopted the traditional microscopic and toxin analyses but not molecular biology and bacterial assemblage approaches. Here we select and optimize the HAB monitoring methodologies suitable for Chilean geography, emphasizing on metabarcoding analyses accompanied by the classical tools with considerations including cost, materials and instrument availability, and easiness and efficiency of performance. We present results from a pilot study using the standardized stepwise protocols, demonstrating feasibility and plausibility for sampling and analysis for the HAB monitoring. Such specific instructions in the standardized protocol are critical obtaining quality data under various research environments involving multiple stations, different analysts, various time-points, and long HAB monitoring duration.

Monitoring harmful microalgal species and their appearance in Tokyo Bay, Japan, using metabarcoding

“…As several genes or markers can be amplified from the same sample, co-appearance patterns and associations amongst species and groups can also be investigated (Lima-Mendez et al 2015;Sawaya et al 2019;Djurhuus et al 2020). This may be especially useful as changes in species diversity, presence of different bacteria and parasites can be monitored continuously over a longer time scale together with the HAB species to recognise changes in those parameters/organism groups as indicators of the state of the HABs (Yang et al 2015;Hattenrath-Lehmann and Gobler 2017;Berdjeb et al 2018;Shin et al 2018;Hattenrath-Lehmann et al 2019;Nagai et al 2019;Jankowiak and Gobler 2020;Yarimizu et al 2020).…”

Relationship between the Microbiome and Indoor Temperature/Humidity in a Traditional Japanese House with a Thatched Roof in Kyoto, Japan

“…The V4 region of the 16S rRNA gene and V9 region of the 18S rRNA gene were used as target regions for sequencing on the Illumina MiniSeq platform. The detailed library preparation procedures are described in [34]. PCR amplification reactions contained 2.5 µL each of 1 µM primers, 12.5 µL of 2× MightyAmp PCR Buffer v. 3 (TaKaRa Clontech, Mountain View, CA, USA), 0.5 µL of MightyAmp DNA Polymerase v.3 (1.25 U/µL), 5 µL of PCR grade water, and 2.5 µL of DNA templates.…”

A Standardized Procedure for Monitoring Harmful Algal Blooms in Chile by Metabarcoding Analysis

“…Chile has been conducting coastal monitoring for many years using two main methods; observing seawater with microscopes to identify toxic algae species regularly and measuring toxin levels in shellfish by biochemical assays 9 .…”

“…has not yet been established in Chilean HAB monitoring 9 . To study algal-bacterial association with HABs, it is imperative to concurrently perform metabarcoding analysis for the current Chilean coastal monitoring programs.…”

“…Thus, this protocol visually introduces our Chilean HAB monitoring program, focusing on a stepwise procedure for analyzing algae and bacteria species detection in seawater samples using metabarcoding analysis. The full protocol describing our Chilean HAB monitoring program is available in Yarimizu et al 9 . It includes the procedures of seawater sampling, microscopic algal species detection, algal-bacterial gene detection, pigment analysis, meteorological data collection, and physical and chemical water property assays.…”