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

Abstract

Harmful algae blooms (HABs) monitoring has been implemented worldwide, and Chile, a country famous for its fisheries and aquaculture, has intensively used microscopic and toxin analyses for decades for this purpose. Molecular biological methods, such as high-throughput DNA sequencing and bacterial assemblage-based approaches, are just beginning to be introduced in Chilean HAB monitoring, and the procedureshave not yet been standardized. Here, 16S rRNA and 18S rRNA metabarcoding analyses for monitoring Chilean HABs are introduced stepwise. According to a recent hypothesis, algal-bacterial mutualistic association plays a critical synergetic or antagonistic relationship accounting for bloom initiation, maintenance, and regression. Thus, monitoring HAB from algal-bacterial perspectives may provide a broader understanding of HAB mechanisms and the basis for early warning. Metabarcoding analysis is one of the best suited molecular-based tools for this purpose because it can detect massive algal-bacterial taxonomic information in a sample. The visual procedures of sampling to metabarcoding analysis herein provide specific instructions, aiming to reduce errors and collection of reliable data.

Monitoring bacterial composition and assemblage in the Gulf of Corcovado, southern Chile: Bacteria associated with harmful algae

“…The sampling methods generally followed the protocol of Yarimizu et al. (2020 , 2021 ). Water was collected at 10-m depth biweekly with a deployed conductivity–temperature–depth (CTD) sampler from a survey ship.…”

“…The analytical methods are described in Yarimizu et al. (2020 , 2021 ). Briefly, nutrient analysis was performed for NO 2 , NO 3 , PO 4 , and Si(OH) 4 using an AQ400 discrete analyzer per United States Environmental Protection Agency (USEPA) procedure 40 C.F.R.…”

“…The oceanographic data, including chl- a, water temperature, salinity, and dissolved oxygen (DO), were transferred from the CTD sampler. DNA was extracted from the filtered membranes using the Chelex-buffer method, followed by high-throughput amplicon sequencing using Illumina MiSeq with the primer sets in Table SII and index primers listed in Yarimizu et al. (2021) .…”

Multitargeted Analyses are Instrumental for Microbial Ecology Studies

“…Studies on the use of metataxonomics (also known as metabarcoding) are fundamental to monitor complex environments and to assemble culturable and unculturable microbial profiles in diverse ecological niches. Yarimizu et al 6 provide a robust methodology to evaluate algal blooms in marine ecosystems and address an important matter in microbial ecology by describing adequate sampling and a strategy for data analysis to make the studies reproducible. Allying microscopy and physicochemical techniques, the authors validate a method to screen seawater samples to detect potential algae species involved with economical losses in the aquaculture of commercial fish products.…”

“…Besides, Masters-Clark et al 8 also show the application of a microfluidics platform based on PDMS to study fungal-fungal and fungal-bacterial interactions in a controlled environment. The main differences between the protocols reside in the design of the channels to accommodate the microorganisms, considering that to reproduce soil geometry and to avoid extreme fungal growth in the matrix, the channels must be carefully evaluated in the protocol of Master-Clark et al 6 , while in the protocol by Pioli et al 5 , the use of colloidal patterning is proposed to calibrate and generate complex multimaterial patterns in the microfluidic matrix design. These studies provide elegant protocols to engineer experiments to model the effective and fundamental ecological niches, which mean the viability of an organism in contact with other organisms in real-life situations and the biotic potential of an organism under ideal conditions to grow, respectively 9 .…”