Hidden aliens: Application of digital <scp>PCR</scp> to track an exotic foraminifer across the Skagerrak (North Sea) correlates well with traditional morphospecies analysis

Morin, Filip; Panova, Marina Antonina Zoe; Schweizer, Magali; Wiechmann, Marlene; Eliassen, Nicole; Sundberg, Per; Cluzel‐Burgalat, Lili; Polovodova Asteman, Irina

doi:10.1111/1462-2920.16458

Cited by 2 publications

(2 citation statements)

References 54 publications

(80 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Also, fluctuations in environmental parameters such as temperature, which could influence the number of rRNA gene copies in ciliates (Fu & Gong, 2017) may impact the accuracy of ciliate abundance measurements via dPCR in natural samples. While for other protistan species, such as foraminifera, cell abundance measurements based on dPCR were highly congruent with classical morphological counts (Morin et al, 2023), such a study is still lacking for free‐living ciliates. Our results suggest, that such a dPCR protocol as available for specific foraminifera could also be developed for ciliates.…”

Section: Discussionmentioning

confidence: 93%

Using digital PCR to predict ciliate abundance from ribosomal RNA gene copy numbers

Gross,

Dunthorn,

Mauvisseau

et al. 2024

Environmental Microbiology

View full text Add to dashboard Cite

Ciliates play a key role in most ecosystems. Their abundance in natural samples is crucial for answering many ecological questions. Traditional methods of quantifying individual species, which rely on microscopy, are often labour‐intensive, time‐consuming and can be highly biassed. As a result, we investigated the potential of digital polymerase chain reaction (dPCR) for quantifying ciliates. A significant challenge in this process is the high variation in the copy number of the taxonomic marker gene (ribosomal RNA [rRNA]). We first quantified the rRNA gene copy numbers (GCN) of the model ciliate, Paramecium tetraurelia, during different stages of the cell cycle and growth phases. The per‐cell rRNA GCN varied between approximately 11,000 and 130,000, averaging around 50,000 copies per cell. Despite these variations in per‐cell rRNA GCN, we found a highly significant correlation between GCN and cell numbers. This is likely due to the coexistence of different cellular stages in an uncontrolled (environmental) ciliate population. Thanks to the high sensitivity of dPCR, we were able to detect the target gene in a sample that contained only a single cell. The dPCR approach presented here is a valuable addition to the molecular toolbox in protistan ecology. It may guide future studies in quantifying and monitoring the abundance of targeted (even rare) ciliates in natural samples.

show abstract

Section: Discussionmentioning

confidence: 93%

Using digital PCR to predict ciliate abundance from ribosomal RNA gene copy numbers

Gross,

Dunthorn,

Mauvisseau

et al. 2024

Environmental Microbiology

View full text Add to dashboard Cite

show abstract

“…Digital PCRs methods such as ddPCR and dPCR provide absolute quantification, i.e. the number of target DNA molecules per µl water, potentially enabling a comparison of eDNA density with other methods of monitoring (Morin et al 2023).…”

Section: Introductionmentioning

confidence: 99%

Monitoring of the invasive round goby in an estuarine seascape based on eDNA

Green,

Dahlgren,

Axberg

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

Non-indigenous species (NIS) is one of the five most global concerns when it comes to ecosystem services and threats to native biodiversity. This is especially true in aquatic environments which are harder to monitor than terrestrial environments, and NIS are often found first when they are fully established and basically impossible to eradicate. In marine environments, this is further complicated due to the connectivity and difficulty of eradication. The development and implementation of effective monitoring methods for marine NIS are therefore crucial to enable early detection useful for management strategies. In this study, we develop and evaluate environmental DNA monitoring using quantitative (q)PCR as a means to assess presence of the euryhaline round goby fish (Neogobius melanostomus) in a seascape environment close to Scandinavia's largest shipping port. We developed a dPCR assay for the species, targeting a region of 12S gene, and verified its specificity compared to other common species from the gobiid-family in the region. We also experimentally determined the decaying rate of round goby DNA in water to a half-life of 9.8 hours in 15 PSU and 15 dC with live fish in captivity. Finally, we sampled 10 sites within a 400 km2 area for eDNA and presence of the species using fyke-nets and baited remote video to validate the accuracy of the water samples to predict presence, and abundance. We found that the number of DNA copies extracted from the water samples varied strongly at sites where round gobies were caught in nets or on video, but that the average value from four water samples significantly correlated with an average value from four video samples, and also with the total catch at each site. The eDNA assay also detected signals from the species at sites where no fish were caught by fishing or on video. These results show that this method is highly sensitive for the species even in low abundance, and with sufficient amounts of replicates, it can be possible to determine the relative abundance between sites.

show abstract

Hidden aliens: Application of digital PCR to track an exotic foraminifer across the Skagerrak (North Sea) correlates well with traditional morphospecies analysis

Cited by 2 publications

References 54 publications

Using digital PCR to predict ciliate abundance from ribosomal RNA gene copy numbers

Using digital PCR to predict ciliate abundance from ribosomal RNA gene copy numbers

Monitoring of the invasive round goby in an estuarine seascape based on eDNA

Contact Info

Product

Resources

About