The use of environmental DNA metabarcoding and quantitative PCR for molecular detection of marine invasive non-native species associated with artificial structures

Gargan, Laura; Brooks, Paul R.; Vye, Siobhan R.; Ironside, Joseph E.; Jenkins, Stuart R.; Crowe, Tasman P.; Carlsson, Jens

doi:10.1007/s10530-021-02672-8

Cited by 22 publications

(14 citation statements)

References 64 publications

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“…Several previous studies have found that amplification bias is a reason for missing some species in eDNA metabarcoding [ 43 , 49 – 51 ]. Normally, amplification bias is thought to be the preferential amplification on some DNA, especially high relative abundance DNA [ 52 – 55 ]. Including the MiFish used in this study, the primers used in eDNA metabarcoding focus on universal sequences to cover a wide range of species.…”

Section: Discussionmentioning

confidence: 99%

Comparison of species-specific qPCR and metabarcoding methods to detect small pelagic fish distribution from open ocean environmental DNA

Ito

Wong

et al. 2022

PLoS ONE

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Environmental DNA (eDNA) is increasingly used to noninvasively monitor aquatic animals in freshwater and coastal areas. However, the use of eDNA in the open ocean (hereafter referred to OceanDNA) is still limited because of the sparse distribution of eDNA in the open ocean. Small pelagic fish have a large biomass and are widely distributed in the open ocean. We tested the performance of two OceanDNA analysis methods—species-specific qPCR (quantitative polymerase chain reaction) and MiFish metabarcoding using universal primers—to determine the distribution of small pelagic fish in the open ocean. We focused on six small pelagic fish species (Sardinops melanostictus, Engraulis japonicus, Scomber japonicus, Scomber australasicus, Trachurus japonicus, and Cololabis saira) and selected the Kuroshio Extension area as a testbed, because distribution of the selected species is known to be influenced by the strong frontal structure. The results from OceanDNA methods were compared to those of net sampling to test for consistency. Then, we compared the detection performance in each target fish between the using of qPCR and MiFish methods. A positive correlation was evident between the qPCR and MiFish detection results. In the ranking of the species detection rates and spatial distribution estimations, comparable similarity was observed between results derived from the qPCR and MiFish methods. In contrast, the detection rate using the qPCR method was always higher than that of the MiFish method. Amplification bias on non-target DNA and low sample DNA quantity seemed to partially result in a lower detection rate for the MiFish method; the reason is still unclear. Considering the ability of MiFish to detect large numbers of species and the quantitative nature of qPCR, the combined usage of the two methods to monitor quantitative distribution of small pelagic fish species with information of fish community structures was recommended.

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Section: Discussionmentioning

confidence: 99%

Comparison of species-specific qPCR and metabarcoding methods to detect small pelagic fish distribution from open ocean environmental DNA

Ito

Wong

et al. 2022

PLoS ONE

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“…In this study, a non-invasive, species-specific detection method, based on eDNA analysis, was successfully developed to monitor the presence of the endangered and elusive Cuvier’s beaked whale in the Canyon of Caprera, and in the wider Tyrrhenian Sea. Although DNA metabarcoding is more useful and cost-efficient when detecting greatest numbers of species at the same time (Gargan et al, 2022), cryptic species needs highly specific and sensitive approaches to be identified (Vörös et al, 2017). Compared to other cetaceans, the Cuvier’s beaked whale is one of the most difficult to study: these animals are able to dive at depth greater than 1 km (Schorr et al, 2014; Gnone et al, 2023) and for extended time period (1 hour, or more), and they also spend short periods at the surface (typically between 2 and 8 minutes) (Baird et al, 2006; Tyack et al, 2006; see also Figure 1).…”

Section: Discussionmentioning

confidence: 99%

Surface-sourced eDNA to track deep-diver cetaceans: the study case of Cuvier’s beaked whale (Ziphius cavirostris) at Caprera Canyon and surrounding areas (Western Mediterranean Sea)

Boldrocchi,

Conte,

Galli

et al. 2023

Preprint

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Among cetaceans, the Cuvier’s beaked whale is considered an extreme diver, very challenging to be studied with standard monitoring methods due to its elusive behaviour and a preference for deep offshore waters. These limitations seem to be mitigated by the use of new molecular methodologies capable of intercepting small traces of DNA left in the environment (eDNA) by marine organisms. Moreover, the collection of water from the superficial layer of the sea represents a perfect case study for the targeting of marine mammals, as the constraints imposed by their nature implies periodic and frequent surfacing. Therefore, we designed and tested a taxon-specific primer set to infer the Cuvier’s beaked whale presence, with the aims of 1) examining the effectiveness of the eDNA technique to detect the presence of deep-diving cetacean in open waters, using the Cuvier’s beaked whale as case study; 2) providing data on the spatiotemporal occurrence of this species within the Canyon of Caprera; and 3) assessing the species occurrence in central northern Mediterranean Sea based on molecular traces. Results from this study demonstrated that collection of superficial waters is a valid approach to monitor deep-diving cetacean species, without the need for complementary visual survey monitoring. Specifically, this study provides evidence of the regular presence of the Cuvier’s beaked whale in the Canyon of Caprera, with a preference for bathymetry in the range of 700-1000 m. This study also showed a potential inshore movement of this species during fall, which is possibly related to migration of its cephalopod prey or a shift in prey preferences. Overall, the data presented here are particularly relevant in the optic of proposing the Caprera Canyon as anImportant Marine Mammal Area(IMMA) in the Mediterranean Sea. At a wider level, this study also showed that the stronger positive signals were recorded in sampling stations located on submarine canyon systems, demonstrating the importance of these areas as elective habitats for the Cuvier’s beaked whale, thus the pivotal priority to their conservation.

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“…Additionally, according to haplotype and genetic difference analysis, we speculated that the introduced sample could have come from Zhejiang and surrounding coastal areas in China. This region was an important coastal city, with developed ports and frequent maritime trade, which could provide a good opportunity for its introduction [ 60 , 61 ]. In addition, Hap1 and its derived haplotypes have recently experienced rapid diffusion and have high environmental adaptability, which provides a good genetic basis for the colonization of this species after introduction [ 62 ].…”

Section: Discussionmentioning

confidence: 99%

Out of East Asia: Early Warning of the Possible Invasion of the Important Bean Pest Stalk-Eyed Seed Bug Chauliops fallax (Heteroptera: Malcidae: Chauliopinae)

Wang

Chen

et al. 2023

Insects

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The short stay at the beginning of the invasion process is a critical time for invasive species identification and preventing invasive species from developing a wider distribution and significant economic impact. The stalk-eyed seed bug Chauliops fallax is an important agricultural pest of soybean and was first reported to occur outside East Asia. Here, we reported the native evolutionary history, recent invasion history, and potential invasion threats of C. fallax for the first time based on population genetic methods and ecological niche modelling. The results showed that four native East Asian genetic groups (EA, WE, TL, and XZ) were well supported, showing an east-west differentiation pattern consistent with the geographical characteristics of three-step landforms in China. Two main haplotypes existed: Hap1 might have experienced a rapid northwards expansion process after the LGM period, and Hap5 reflected local adaptation to the environment in southeastern China. The Kashmir sample was found to come from the recent invasion of populations in the coastal areas of southern China. Ecological niche modelling results suggested that North America has a high risk of invasion, which might pose a serious threat to local soybean production. In addition, with future global warming, the suitable habitat in Asia will move towards the higher latitude region and gradually deviate from the soybean planting area, which indicates the threat of C. fallax to soybean production in Asia will decrease in the future. The results could provide new insights into the monitoring and management of this agricultural pest in the early invasion stage.

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The use of environmental DNA metabarcoding and quantitative PCR for molecular detection of marine invasive non-native species associated with artificial structures

Cited by 22 publications

References 64 publications

Comparison of species-specific qPCR and metabarcoding methods to detect small pelagic fish distribution from open ocean environmental DNA

Comparison of species-specific qPCR and metabarcoding methods to detect small pelagic fish distribution from open ocean environmental DNA

Surface-sourced eDNA to track deep-diver cetaceans: the study case of Cuvier’s beaked whale (Ziphius cavirostris) at Caprera Canyon and surrounding areas (Western Mediterranean Sea)

Out of East Asia: Early Warning of the Possible Invasion of the Important Bean Pest Stalk-Eyed Seed Bug Chauliops fallax (Heteroptera: Malcidae: Chauliopinae)

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