Fish environmental DNA in Tokyo Bay: A feasibility study on the availability of environmental DNA for fisheries

Hongo, Yuki; Nishijima, Shota; Kanamori, Yuki; Sawayama, Shuhei; Yokouchi, Kazuki; Kanda, Natsuki; Oori, Shiori; Uto, Yasuyuki; Ishii, Mitsuhiro; Mita, Hisanori; Akimoto, Seiji; Kusano, Akane; Okabe, Kyu; YAMAZAKI, TETSUYA; Fukuda, Naoko; Onitsuka, Toshihiro; Minagawa, Masayuki; Okamura, Hiroshi; Niwa, Koichi; Nagai, Satoshi; Suzuki, Shigenori; Yoneda, Michio; Yamamoto, Toshihiro; Kurogi, Hiroaki

doi:10.1016/j.rsma.2021.101950

Cited by 9 publications

(11 citation statements)

References 31 publications

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“…We obtained 308 water samples for the eDNA extraction, and gene amplification were successful for 281 samples, from which about 28 M reads were obtained and approximately 4 M reads were assigned as fish species (Hongo et al, 2021). The gene amplifications were not detected from negative control filters.…”

Section: Resultsmentioning

confidence: 99%

“…The frozen filters were then transferred to and stored in the laboratory. The extraction of eDNA and the construction of amplicon sequencing variants (ASVs) were performed as described by Hongo et al (2021) using MiFish universal primers (Miya et al, 2015). One sample replicate on the field, and one PCR replicate per sample was conducted in this study.…”

Section: Methodsmentioning

confidence: 99%

“…This is because the extremely severe environment in the bottom negatively affects fish occurrences irrespective of the species identity and thus the severity does not operate as ‘species’ sorting (Figure 1b), which leads to the mixing of species composition. To this end, we took advantage of the availability of data of seasonal dynamics of fish communities in Tokyo Bay revealed by the environmental DNA (eDNA) metabarcoding analysis (Hongo et al, 2021) which has emerged as a powerful and efficient tool for monitoring biodiversity especially in aquatic ecosystems (Bohmann et al, 2014; Deiner et al, 2017). By extracting genetic materials shed from organisms from environmental samples (e.g., water and soils), this technique allows for the noninvasive assessment of biodiversity, with a detection ability comparable or superior to that of traditional sampling methods (Sigsgaard et al, 2017; Thomsen et al, 2012; Yamamoto et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

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Similar fish species composition despite larger environmental heterogeneity during severe hypoxia in a coastal ecosystem

Shinohara

Hongo

Ichinokawa

et al. 2022

Ecology and Evolution

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Environmental heterogeneity is one of the most influential factors that create compositional variation among local communities. Greater compositional variation is expected when an environmental gradient encompasses the most severe conditions where species sorting is more likely to operate. However, evidence for stronger species sorting at severer environment has typically been obtained for less mobile organisms and tests are scarce for those with higher dispersal ability that allows individuals to sensitively respond to environmental stress. Here, with the dynamics of fish communities in a Japanese bay revealed by environmental DNA metabarcoding analyses as a model case, we tested the hypothesis that larger environmental heterogeneity caused by severe seasonal hypoxia (lower concentration of oxygen in bottom waters in summer) leads to larger variation of species composition among communities. During summer, fish species richness was lower in the bottom layer, suggesting the severity of the hypoxic bottom water. In contrast to the prediction, we found that although the environmental parameters of bottom and surface water was clearly distinct in summer, fish species composition was more similar between the two layers. Our null model analysis suggested that the higher compositional similarity during hypoxia season was not a result of the sampling effect reflecting differences in the alpha or gamma diversity. Furthermore, a shift in the species occurrence from bottom to surface layers was observed during hypoxia season, which was consistent across species, suggesting that the severe condition in the bottom adversely affected fish species irrespective of their identity. These results suggest that larger environmental heterogeneity does not necessarily lead to higher compositional variation once the environmental gradient encompasses extremely severe conditions. This is most likely because individual organisms actively avoided the severity quasi‐neutrally, which induced mass effect‐like dispersal and lead to the mixing of species composition across habitats. By showing counter evidence against the prevailing view, we provide novel insights into how species sorting by environment acts in heterogeneous and severe conditions.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Similar fish species composition despite larger environmental heterogeneity during severe hypoxia in a coastal ecosystem

Shinohara

Hongo

Ichinokawa

et al. 2022

Ecology and Evolution

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“…For example, Levi et al (2019) determined that at-least daily eDNA sampling was required to capture the ephemeral migration and spawning of anadromous salmonids in an Alaskan stream. Long-term (i.e., on the order of seasons to years) observations of fish assemblage patterns conducted using traditional methods are commonly used to inform conservation efforts and determine how species respond to chronic threats such as climate change (Adams et al, 2011;Quinn, 2018), yet long-term eDNA studies are few and those that exist are often conducted at the expense of sampling interval (Doi et al, 2017;Hongo et al, 2021;Pilliod et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

“…There have been many attempts to relate eDNA concentrations with organism abundance (Rourke et al, 2021), but the results of those studies are equivocal. While many studies have shown empirically that eDNA concentrations in water samples correlate positively with more traditional measures of organism abundance (Doi et al, 2017; Pilliod et al, 2013; Shelton et al, 2019; Takahara et al, 2012; Tillotson et al, 2018), some indicate no correlation (Capo et al, 2019; Hinlo et al, 2018; Hongo et al, 2021; Perez et al, 2017). The discrepant results between different studies could be attributable to variable source strength (i.e., abundance or biomass) of the target organism, as well as differences in the fate and transport of eDNA in different systems.…”

Section: Introductionmentioning

confidence: 99%

High‐frequency and long‐term observations of eDNA from imperiled salmonids in a coastal stream: Temporal dynamics, relationships with environmental factors, and comparisons with conventional observations

et al. 2022

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A greater understanding of eDNA behavior in the environment is needed before it can be employed for ecosystem monitoring applications. The objectives of this study were to use autonomous sampling to conduct long‐term, high‐frequency monitoring of the eDNA of native salmonid species in a Californian coastal stream, describe temporal variation of eDNA on multiple scales and identify environmental factors that drive this variation, and evaluate the ability of the eDNA datasets to detect rare species and represent organismal abundance. Using high‐throughput autonomous environmental sample processors (ESPs) and qPCR, we enumerated eDNA concentrations from 674 water samples collected at subdaily intervals over 360 days at a single site. We detected eDNA from two imperiled salmonids (coho salmon Oncorhynchus kisutch and steelhead/rainbow trout O. mykiss) in most samples; O. kisutch eDNA was generally in lower concentration and more variable than O. mykiss eDNA. High‐frequency (i.e., subdaily and daily) variability in salmonid eDNA concentrations showed occasional patchiness (i.e., large differences between consecutive samples), while seasonal differences were observed consistent with the ecology of the species at this site. Salmonid eDNA concentrations were significantly associated with creek discharge, photoperiod, and whether the creek mouth was open or closed by a seasonal sandbar. The release of hatchery‐origin O. kisutch parr into the stream was associated with a significant increase in eDNA concentration for the remainder of the study. We compared eDNA signals with fish abundance data collected from traps located at the site. Fish were detected more often by eDNA than from trapping. Significant positive associations between fish abundance and eDNA concentrations were observed for O. mykiss; however, no such associations were observed for O. kisutch. This study adds to our knowledge on the occurrence and behavior of fish eDNA in lotic systems and informs future biomonitoring efforts using automated sampling technology.

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Using eDNA to estimate biomass of bycatch in pelagic fisheries

et al. 2022

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In recent years, the analysis of environmental DNA (eDNA) has significantly improved, allowing for high‐resolution species identification and possible biomass quantification from water samples. Fisheries management typically requires monitoring of catches, including precise information about bycatch quantities to make sound assessments of exploitation rates. Bycatch assessment is particularly challenging in large catches (>500 T), and the current practice of visual assessment of subsampled catches is time‐consuming, requires extensive labor, and often has low precision. We explored the feasibility for applying eDNA‐based methods for studying catch composition using the pelagic North Sea herring fishery with bycatch of mackerel as a case. First, we experimentally simulate a series of catches using a range of herring and mackerel weight proportions to establish relationships under real fisheries scenarios. The relationship is subsequently used to estimate the biomass of mackerel bycatch from eDNA from three herring catches, by sampling and comparing processing water both onboard ships and at the processing factory. All samples are analyzed using species‐specific quantitative PCR (qPCR). The experiments reveled a strong correlation between DNA and weight fractions characterized by a constant overrepresentation of mackerel DNA compared to expected mackerel weight. We found that eDNA‐based and visual methods applied to the same landing reflect the within catch variability in species composition alike, however, the methods can show disparity in total estimates of mackerel biomass. Accounting for haul mixing within total landed catches increases the precision of the factory and ship eDNA‐based estimates for the same catch. We show that eDNA‐based bycatch estimates provide coherent quantitative data, and likely improve quality and reduce costs of collecting fisheries‐dependent data and thereby contribute to securing sustainable fisheries.

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Fish environmental DNA in Tokyo Bay: A feasibility study on the availability of environmental DNA for fisheries

Cited by 9 publications

References 31 publications

Similar fish species composition despite larger environmental heterogeneity during severe hypoxia in a coastal ecosystem

Similar fish species composition despite larger environmental heterogeneity during severe hypoxia in a coastal ecosystem

High‐frequency and long‐term observations of eDNA from imperiled salmonids in a coastal stream: Temporal dynamics, relationships with environmental factors, and comparisons with conventional observations

Using eDNA to estimate biomass of bycatch in pelagic fisheries

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