Targeted non-invasive bioindicator species detection in eDNA water samples to assess and monitor the integrity of vulnerable alpine freshwater environments

Blattner, Lucas; Ebner, Joshua Niklas; Zopfi, Jakob; Fumetti, Stefanie von

doi:10.1016/j.ecolind.2021.107916

Cited by 21 publications

(17 citation statements)

References 100 publications

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“…Use of eDNA can greatly complement traditional species monitoring by enabling greater taxonomic resolution (Deiner et al 2017;Ruppert et al 2019), the detection of species which tend to avoid the presence of humans (Yonezawa et al 2020;Mas-Carrió et al 2021), or organisms such as bacteria and fungi which can be difficult to monitor using traditional observations (Frøslev et al 2019;Liddicoat et al 2022). Comparisons of eDNA with observational methods have also indicated their potential to help capture additional elements of ecologically relevant information, such as the functional diversity of various groups of species (Aglieri et al, 2021;Donald et al 2021;Sigsgaard et al 2021), particularly with regards to identifying ecological indicators (Yan et al 2018;Blattner et al 2021;Seymour et al 2021).…”

Section: Future Prospectsmentioning

confidence: 99%

Constructing ecological indices for urban environments using species distribution models

Simons

CALDWELL

et al. 2022

Urban Ecosyst

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In an increasingly urbanized world, there is a need to study urban areas as their own class of ecosystems as well as assess the impacts of anthropogenic impacts on biodiversity. However, collecting a sufficient number of species observations to estimate patterns of biodiversity in a city can be costly. Here we investigated the use of community science-based data on species occurrences, combined with species distribution models (SDMs), built using MaxEnt and remotely-sensed measures of the environment, to predict the distribution of a number of species across the urban environment of Los Angeles. By selecting species with the most accurate SDMs, and then summarizing these by class, we were able to produce two species richness models (SRMs) to predict biodiversity patterns for species in the class Aves and Magnoliopsida and how they respond to a variety of natural and anthropogenic environmental gradients.We found that species considered native to Los Angeles tend to have significantly more accurate SDMs than their non-native counterparts. For all species considered in this study we found environmental variables describing anthropogenic activities, such as housing density and alterations to land cover, tend to be more influential than natural factors, such as terrain and proximity to freshwater, in shaping SDMs. Using a random forest model we found our SRMs could account for approximately 54% and 62% of the predicted variation in species richness for species in the classes Aves and Magnoliopsida respectively. Using community science-based species occurrences, SRMs can be used to model patterns of urban biodiversity and assess the roles of environmental factors in shaping them.

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Section: Future Prospectsmentioning

confidence: 99%

Constructing ecological indices for urban environments using species distribution models

Simons

CALDWELL

et al. 2022

Urban Ecosyst

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“…Finally, studies such as ours will be helpful in the near future for members of the community who work on biomonitoring based on metabarcoding or environmental DNA. We might cite the recent article from Blattner et al 25 , which includes Hygrobates norvegicus among other bioindicator species. This study was based on the www.nature.com/scientificreports/ amplification of several mitochondrial genes.…”

Section: Discussionmentioning

confidence: 99%

Complete mitochondrial genome of Hygrobates turcicus Pešić, Esen & Dabert, 2017 (Acari, Hydrachnidia, Hygrobatoidea)

Zawal

Skuza

Michoński

et al. 2022

Sci Rep

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The aim of the study was sequencing of the mitogenome of Hygrobates turcicus Pešić, Esen & Dabert, 2017 to expand knowledge of the polymorphism and cryptic or pseudocryptic diversity within Hydrachnidia. The samples originated from Bulgaria, Vidima River near Debnewo, 42°56′41.4′′N, 24°48′44.6′′E, depth 0.4 m, stones on the bottom, water flow 0.71 m/s, temperature 10 °C, pH 8.53, oxygen 110%, conductivity 279 µS/cm, hardness 121 CaO mg/l; 11 males, 27 females, 2 deutonymphs 12.x.2019 leg. Zawal, Michoński & Bańkowska; one male and one female dissected and slides mounted. The study was carried out using the following methods: DNA extraction, sequencing, assembly and annotation, comparison with other populations of H. turcicus, and multigene phylogeny. As a result of the study, it was determined that the mitogenome is 15,006 bp long and encodes for 13 proteins, 2 rRNAs, and 22 tRNAs. The genome is colinear with those of H. longiporus and H. taniguchii, the difference in size originating from a non-coding region located between protein-coding genes ND4L and ND3. Five genes have alternative start-codon, and four display premature termination. The multigene phylogeny obtained using all mitochondrial protein-coding genes unambiguously associates H. turcicus with the cluster formed by H. longiporus and H. taniguchii.

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“…Bioassessment of freshwater environments based on environmental DNA (eDNA) is an important application of metabarcoding. It is increasingly used to complement traditional approaches (Blattner et al, 2021; Kutty et al, 2022; Schenekar, 2022), which involve the collection and identification of metazoan taxa such as macroinvertebrates, zooplankton, and fishes (Resh, 2008; Roux et al, 1993). Bioassessment with eDNA is particularly attractive in that it is less invasive and does not require costly manual specimen collection, sorting, and identification with morphological tools.…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Toward eDNA‐based bioassessment of freshwater reservoirs with small volumes of water: Robust molecular protocols

et al. 2022

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Bioassessment of freshwater quality with eDNA is a powerful alternative to traditional methods involving collecting, sorting, and identifying metazoan taxa with morphology (e.g., macroinvertebrates). Particularly attractive for routine monitoring would be an eDNA method that uses a remote-controlled boat for collecting small volumes of water without filtration in order to simplify sampling. Such a method would not likely capture eDNA signals for all metazoan species, but may nevertheless allow for cost-effective, and frequent monitoring of water quality, which is important for tropical waterbodies that require year-round surveillance. We here optimize a molecular protocol for capturing metazoan signatures based on eDNA obtained from 15 ml of water. To test the robustness of the method, we used samples from two tropical reservoirs with known differences in water quality to optimize molecular procedures so that they yield repeatable results. Each reservoir was sampled at three sites ("biological replicates") and each water sample was subsampled twice before extracting the eDNA using ethanol precipitation for both subsamples ("technical replicates"). We then tested how much DNA (0.1 ng to 15 ng) and how many PCR cycles (25 or 35) minimized the variance of the metazoan eDNA signal between biological and technical replicates. For this purpose, we amplified a 313 bp COI minibarcode using a universal metazoan primer pair. We found that regardless of template amounts or PCR cycle numbers, the eDNA signatures for both reservoirs were distinct because only 17 of 59 mOTUs (mainly planktonic crustaceans and rotifers) were shared. We also found that template amounts between 0.5 and 15 ng yielded overall similar results, but the use of 35 PCR cycles significantly depressed the number of detected species (p-value < 0.05). Fortunately, the differences between the detected metazoan community of the reservoirs were so strong that all biological and technical replicates could be assigned unambiguously to their source reservoir although the variance between technical replicates remained high for all PCR experiments (Bray-Curtis dissimilarity: 5%-20%; Jaccard distance: 10%-40%).

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Targeted non-invasive bioindicator species detection in eDNA water samples to assess and monitor the integrity of vulnerable alpine freshwater environments

Cited by 21 publications

References 100 publications

Constructing ecological indices for urban environments using species distribution models

Constructing ecological indices for urban environments using species distribution models

Complete mitochondrial genome of Hygrobates turcicus Pešić, Esen & Dabert, 2017 (Acari, Hydrachnidia, Hygrobatoidea)

Toward eDNA‐based bioassessment of freshwater reservoirs with small volumes of water: Robust molecular protocols

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