Monitoring fish communities through environmental DNA metabarcoding in the fish pass system of the second largest hydropower plant in the world

New insights into biologic interpretation of bioinformatic pipelines for fish eDNA metabarcoding: A case study in Pearl River estuary

Environmental DNA (eDNA) metabarcoding is an emerging tool for monitoring biological communities in aquatic ecosystems. The selection of bioinformatic pipelines significantly impacts the results of biodiversity assessments. However, there is currently no consensus on the appropriate bioinformatic pipelines for fish community analysis in eDNA metabarcoding. In this study, we compared three bioinformatic pipelines (Uparse, DADA2, and UNOISE3) using real and mock (constructed with 15/30 known fish) communities to investigate the differences in biological interpretation during the data analysis process in eDNA metabarcoding. Performance evaluation and diversity analyses revealed that the choice of bioinformatic pipeline could impact the biological results of metabarcoding experiments. Among the three pipelines, the operational taxonomic units (OTU)-based pipeline (Uparse) showed the best performance (sensitivity: 0.6250 ± 0.0166; compositional similarity: 0.4000 ± 0.0571), the highest richness (25-102) and minimal inter-group differences in alpha diversity. It suggested the OTU-based pipeline possessed superior capability in fish diversity monitoring compared to ASV/ZOTU-based pipeline. Additionally, the Bray-Curtis distance matrix achieved the highest discriminative effect in the PCoA (43.3%-53.89%) and inter-group analysis (P < 0.01), indicating it was better at distinguishing compositional differences or specific genera of fish community at different sampling sites than other distance matrices. These findings provide new insights into fish community monitoring through eDNA metabarcoding in estuarine environments.

Improving the efficiency of adaptive management methods in multiple fishways using environmental DNA

Dams and weirs impede the continuity of rivers and transit of migratory fish. To overcome this obstacle, fishways are installed worldwide; however, management after installation is important. The Miyanaka Intake Dam has three fish ladders with different flow velocities and discharges and has been under adaptive management since 2012. Fish catch surveys, conducted as an adaptive management strategy, place a heavy burden on fish. Furthermore, a large number of investigators must be mobilized during the 30-day investigation period. Thus, a monitoring method using environmental DNA that exerts no burden on fish and requires only a few surveyors (to obtain water samples) and an in-house analyst was devised; however, its implementation in a fishway away from the point of analysis and with limited flow space and its effective water sampling frequency have not been reported. Therefore, in 2019, we started a trial aiming to evaluate the methods and application conditions of environmental DNA surveys for the continuous and long-term monitoring of various fish fauna upstream and downstream of the Miyanaka Intake Dam. To evaluate the fish fauna, the results of an environmental DNA survey (metabarcoding method) for 2019 to 2022 were compared to those of a catch survey in the fishway from 2012 to 2022. The results confirmed the use of environmental DNA surveys in evaluating the contribution of fishways to biodiversity under certain conditions and introduced a novel method for sample collection.

Pragmatic applications of DNA barcoding markers in identification of fish species – a review

DNA barcoding and mini barcoding involve Cytochrome Oxidase Subunit I (COI) gene in mitochondrial genome and is used for accurate identification of species and biodiversity. The basic goal of the current study is to develop a complete reference database of fishes. It also evaluates the applicability of COI gene to identify fish at the species level with other aspects i.e., as Kimura 2 parameter (K2P) distance. The mean observed length of the sequence was ranging between 500 to 700 base pairs for fish species in DNA barcoding and 80 to 650 base pairs for DNA mini barcoding. This method describes the status of known to unknown samples but it also facilitates the detection of previously un-sampled species at distinct level. So, mini-barcoding is a method focuses on the analysis of short-length DNA markers has been demonstrated to be effective for species identification of processed food containing degraded DNA. While DNA meta-barcoding refers to the automated identification of multiple species from a single bulk sample. The may contain entire organisms or a single environmental sample containing degraded DNA. Despite DNA barcoding, mini barcoding and meta-barcoding are efficient methods for species identification which are helpful in conservation and proper management of biodiversity. It aids researchers to take an account of genetic as well as evolutionary relationships by collecting their morphological, distributional and molecular data. Overall, this paper discusses DNA barcoding technology and how it has been used to various fish species, as well as its universality, adaptability, and novel approach to DNA-based species identification.