Seasonal changes in the distribution of black sea bream Acanthopagrus schlegelii estimated by environmental DNA

Sasano, Sachia; Murakami, Hiroaki; Suzuki, Keita W.; Minamoto, Toshifumi; Yamashita, Yoh; Masuda, Reiji

doi:10.1007/s12562-021-01572-z

Cited by 8 publications

(4 citation statements)

References 52 publications

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“…False negatives could lead to delayed implementation of eradication programs for invasive species or overlooking remnant populations of threatened species. Many eDNA studies have not reported use of positive controls (for example, Rusch et al., 2020; Sasano et al., 2022; Zirngibl et al., 2022), or have used exogenous positive controls designed only for assessing reliability of PCR amplification (for example Pilliod et al., 2013; Wilcox et al., 2015; Wilson et al., 2014). However, this type of positive control can only be used to monitor PCR errors but not errors in the preceding steps required for sampling and handing of eDNA in preparation for PCR.…”

Section: Discussionmentioning

confidence: 99%

Generic qPCR assays for quality control in environmental DNA research

Zhu,

Bell,

Rourke

et al. 2024

Environmental DNA

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Environmental DNA (eDNA) has been widely used for species surveillance. However, the lack of adequate quality control in many eDNA research projects and applications can lead to false‐negative results, greatly affecting biosecurity surveillance and conservation efforts. Exogenous DNA is routinely added to eDNA samples and used as a positive control, typically after DNA extraction. However, this type of positive control is only able to identify false negatives due to errors at the amplification stage. Therefore, errors in upstream processes, such as sample collection will not be identified by an exogenous control. We designed two independent sets of generic quality control qPCR assays (QCqPCR) targeting abundant endogenous DNA that is obtained during sample collection. Our QCqPCR assays target the chloroplast 16S and 23S ribosomal RNA sequences. In silico analyses indicated these regions were highly conserved among plants, algae and bacteria commonly found in freshwater, marine, or terrestrial environments. These QCqPCR assays were purposely mismatched against the human genome to avoid false positives resulting from human DNA contamination. Both assays remained highly efficient and sensitive under annealing temperatures between 58 and 62°C, allowing them to be multiplexed with most qPCR analyses. We validated our assays by multiplexing with a species‐specific Murray cod (Maccullochella peelii) assay on field‐collected environmental water samples. Potential false‐negative reactions can be identified by the failed or suppressed QCqPCR assay and the negative species‐specific assay. We recommend incorporating either one of the QCqPCR assays in qPCR‐based eDNA analysis to identify potential false negatives and improve the reliability of eDNA surveys.

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Section: Discussionmentioning

confidence: 99%

Generic qPCR assays for quality control in environmental DNA research

Zhu,

Bell,

Rourke

et al. 2024

Environmental DNA

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“…The primers and probe were designed to specifically amplify a 129-bp fragment from the A. schlegelii mitochondrial cytochrome b (cyt b ) gene ( Takahashi et al, 2020 ). The species specificity of the primers and probe was checked by Sasano et al, 2022 . Reaction conditions were as follows: 10 min at 95°C, 55 cycles at 95°C for 10 s, and at 60°C for 30 s. PCR triplicates were provided for each sample.…”

Section: Methodsmentioning

confidence: 99%

Temperature sensitivity of the interspecific interaction strength of coastal marine fish communities

Ushio

Sadõ

Fukuchi

et al. 2023

eLife

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The effects of temperature on interaction strengths are important for understanding and forecasting how global climate change impacts marine ecosystems; however, tracking and quantifying interactions of marine fish species is practically difficult especially under field conditions, and thus, how temperature influences their interaction strengths under field conditions remains poorly understood. We herein performed quantitative fish environmental DNA (eDNA) metabarcoding on 550 seawater samples that were collected twice a month from 11 coastal sites for two years in the Boso Peninsula, Japan, and analyzed eDNA monitoring data using nonlinear time-series analytical tools. We detected fish-fish interactions as information flow between eDNA time series, reconstructed interaction networks for the top 50 frequently detected species, and quantified pairwise, fluctuating interaction strengths using nonlinear time series analysis methods. Although there was a large variation, water temperature generally influenced fish-fish interaction strengths. The impact of water temperature on interspecific interaction strengths varied among fish species, suggesting that fish species identity influences the temperature effects on interactions. For example, interaction strengths that Halichoeres tenuispinis and Microcanthus stringatus received strongly increased with water temperature, while those of Engraulis japonicus and Girella punctata decreased with water temperature. An increase in water temperature induced by global climate change may change fish interactions in a complex way, which consequently influences marine community dynamics and stability. Our research demonstrates a practical research framework to study the effects of environmental variables on interaction strengths of marine communities under field conditions, and thus, would contribute to further understanding and predicting natural marine ecosystem dynamics.

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“…Through the eDNA analysis, and incorporating principal component analysis, a multiple regression tree model, and Mantel tests, we identified temperature as a key environmental factor influencing both warm-water and cold-water fish communities (Figure S2). Species such as Acanthopagrus schlegelii and Pagrus major, endemic to the Seto Inland Sea, exhibit ecological attributes that enable adaptation to diverse temperature and salinity conditions, indicative of their high physiological adaptability [76][77][78][79]. While these species were detected across seasons, their relative abundance exhibited seasonal variation (Table S3).…”

Section: Controlling Factors Of the Seasonal Fluctuations In Fish Com...mentioning

confidence: 99%

Evaluation of the Effects of Environmental Factors on Seasonal Variations in Fish Diversity on a Coastal Island in Western Japan

Nhat,

Saito,

Hamada

et al. 2024

Environments

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Coastal habitats are crucial for supporting ecological processes and serve as vital ecosystems for diverse fish species, providing essential functions such as feeding, nursery provision, and reproductive habitats. Fish communities are ecologically important components of coastal ecosystems and are affected by multiple environmental factors. Despite their importance, determining the effects of environmental factors on seasonal variations in fish species diversity and community dynamics remains a challenge. The advent of environmental DNA (eDNA) technology, an environmentally conscious approach, has resulted in considerable advancements in recent years and has been progressively adopted for marine fish population monitoring. Here, we used environmental DNA metabarcoding to study seasonal variations in fish community structure on a coastal island, and we assessed the effects of environmental factors in structuring these communities. Our findings revealed a rich diversity of 72 fish species across 40 families and 23 orders in the seawater surrounding an island of the Seto Inland Sea (SIS), Western Japan. Notably, the composition of fish communities varied significantly between seasons, with seawater temperature, salinity, and dissolved inorganic phosphorus (DIP) concentration identified as important factors correlated with fish communities’ structures. In conclusion, our study provides useful information of fish diversity, and we suggest that eDNA is a valuable technique for monitoring fish diversity in coastal areas. These findings are crucial for ecological studies and the environmental monitoring of oceanic coastal environments.

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Seasonal changes in the distribution of black sea bream Acanthopagrus schlegelii estimated by environmental DNA

Cited by 8 publications

References 52 publications

Generic qPCR assays for quality control in environmental DNA research

Generic qPCR assays for quality control in environmental DNA research

Temperature sensitivity of the interspecific interaction strength of coastal marine fish communities

Evaluation of the Effects of Environmental Factors on Seasonal Variations in Fish Diversity on a Coastal Island in Western Japan

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