Positive effect of filtration additives for increasing environmental DNA detections in summer and winter oceanic waters

Ahn, Hyojin; Asano, Y.; Suzuki, Shota; Ooki, Atsushi

doi:10.1002/edn3.282

Cited by 4 publications

(5 citation statements)

References 53 publications

(65 reference statements)

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“…Along with filtration volume, the number of replicates of filtered samples is also an important factor for estimating biodiversity using eDNA metabarcoding analysis. The source of eDNA in seawater exhibits sporadic distribution, and the estimation of biodiversity using eDNA is strongly influenced by the sampling effort (Bessey et al, 2020;Stauffer et al, 2021;Ahn et al, 2022). The number of detected species was relatively congruent among replicates, with a variation of up to 8 species between replicates for the Akazawa samples and up to 12 species between replicates for the Yaizu samples.…”

Section: Discussionmentioning

confidence: 99%

Optimization of environmental DNA analysis using pumped deep-sea water for the monitoring of fish biodiversity

Yoshida

Kawato²,

Fujiwara³

et al. 2023

Front. Mar. Sci.

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Deep-sea ecosystems present difficulties in surveying and continuous monitoring of the biodiversity of deep-sea ecosystems because of the logistical constraints, high cost, and limited opportunities for sampling. Environmental DNA (eDNA) metabarcoding analysis provides a useful method for estimating the biodiversity in aquatic ecosystems but has rarely been applied to the study of deep-sea fish communities. In this study, we utilized pumped deep-sea water for the continuous monitoring of deep-sea fish communities by eDNA metabarcoding. In order to develop an optimum method for continuous monitoring of deep-sea fish biodiversity by eDNA metabarcoding, we determined the appropriate amount of pumped deep-sea water to be filtered and the practical number of filtered sample replicates required for biodiversity monitoring of deep-sea fish communities. Pumped deep-sea water samples were filtered in various volumes (5–53 L) at two sites (Akazawa: pumping depth 800 m, and Yaizu: pumping depth 400 m, Shizuoka, Japan) of deep-sea water pumping facilities. Based on the result of evaluations of filtration time, efficiency of PCR amplification, and number of detected fish reads, the filtration of 20 L of pumped deep-sea water from Akazawa and filtration of 10 L from Yaizu were demonstrated to be suitable filtration volumes for the present study. Fish biodiversity obtained by the eDNA metabarcoding analyses showed a clear difference between the Akazawa and Yaizu samples. We also evaluated the effect of the number of filter replicates on the species richness detected by eDNA metabarcoding from the pumped deep-sea water. At both sites, more than 10 sample replicates were required for the detection of commonly occurring fish species. Our optimized method using pumped deep-sea water and eDNA metabarcoding can be applied to eDNA-based continuous biodiversity monitoring of deep-sea fish to better understand the effects of climate change on deep-sea ecosystems.

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Section: Discussionmentioning

confidence: 99%

Optimization of environmental DNA analysis using pumped deep-sea water for the monitoring of fish biodiversity

Yoshida

Kawato²,

Fujiwara³

et al. 2023

Front. Mar. Sci.

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“…In this study we conducted extensive eDNA sampling both spatially and temporally, covering locations and habitats with previous E. akaara distribution records, as well as local marine protected areas where neither recreational nor commercial fishing is permitted. We also deployed sampling methods that can increase captured diversity thus maximizing the likelihood of detecting this locally rare species, including sampling seawater along a 2km coastline transect, and large filter volume instead of several replicates of smaller volume (Ahn et al, 2022; Mathon et al, 2023). Despite the efforts, we could barely detect target species eDNA in the environmental seawater samples with qPCR, with only 6 samples (6.82%) in total showing minimal traces of target species eDNA.…”

Section: Discussionmentioning

confidence: 99%

Novel assay for endangered Hong Kong grouper (Epinephelus akaara) to assess eDNA shedding, decay, and population status

Chung,

Kam,

Schunter

2024

Preprint

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Overexploitation is a major threat to marine ecosystems, causing collapse of numerous fisheries since the 19th century. The Hong Kong Grouper (Epinephelus akaara) is a commercial fish species that suffered at least 50-80% population declines in the past 40 years throughout its distribution range. Yet there has been minimal research or specific management, resulting in insufficient data on abundance, reproduction and habitat utilization. Here we aim to develop a novel species-specific quantitative PCR (qPCR) assay to detect potential occurrence of E. akaara through non-invasive environmental water samples. We developed a qPCR assay amplifying 71 bps of the mitochondrial ND2 gene which offers high sensitivity and specificity. To quantify the E. akaara population with the emerging environmental DNA (eDNA) tool, however, species-specific shedding and decay rates are crucial. The decay rate of E. akaara was similar to that of reported values of other marine fish species. However, the shedding rate of E. akaara was found to be few orders of magnitude lower which may be related to the relatively low activity and energy use from solitary and sedentary behavior of groupers. This highlights the importance of empirically determining species or taxon-specific shedding and decay rates to inform accurate abundance estimates with modelling tools for eDNA concentrations. Only 6 out of 88 water samples (6.81%) collected across 4 sampling seasons and 11 sites around Hong Kong showed positive signals at a concentration below limit of detection of the assay, implying its rarity in Hong Kong nowadays. Overall, we demonstrate that eDNA with our qPCR assay is efficient and sensitive in detecting the target species and is a promising tool in documenting endangered species for species management and conservation.

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“…Moreover, there was no indication of human-derived contamination in any of the filters examined. Given the sporadic distribution of eDNA sources in seawater [1] , [2] , [3] , the detection of species using eDNA is significantly influenced by this sporadicity [5] . Consistent with previous findings showing variability in the number of fish species detected from filters collected under identical water conditions in Yaizu [5] , this study is expected to reveal similar variability.…”

Section: Methods Validationmentioning

confidence: 99%

“…The filtration process used to collect eDNA from the water samples is essential for eDNA analysis. eDNA is sporadically distributed [1] , [2] , [3] , and in deep-sea water, it is present in trace amounts owing to the lower organism density compared to shallow waters [4] . Consequently, effective biodiversity monitoring in deep-sea environments requires both a large volume of filtration (e.g., 10–20 L per filter) and multiple filtration replicates (e.g., up to 10) for an accurate assessment of biodiversity in surveyed habitats [5 , 6] .…”

Section: Introductionmentioning

confidence: 99%

Rapid, contamination-less, and efficient environmental DNA filtration system

Yoshida,

Yamazaki,

Kawato

et al. 2024

MethodsX

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Positive effect of filtration additives for increasing environmental DNA detections in summer and winter oceanic waters

Cited by 4 publications

References 53 publications

Optimization of environmental DNA analysis using pumped deep-sea water for the monitoring of fish biodiversity

Optimization of environmental DNA analysis using pumped deep-sea water for the monitoring of fish biodiversity

Novel assay for endangered Hong Kong grouper (Epinephelus akaara) to assess eDNA shedding, decay, and population status

Rapid, contamination-less, and efficient environmental DNA filtration system

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