Stirring up the relationship between quantified environmental DNA concentrations and exoskeleton‐shedding invertebrate densities

Trimbos, Krijn B.; Cieraad, Ellen; Schrama, Maarten; Saarloos, Aagje I.; Musters, K.; Bertola, Laura D.; Bodegom, Peter M. van

doi:10.1002/edn3.157

Cited by 7 publications

(4 citation statements)

References 88 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…There are also several knowledge gaps surrounding the use of eDNA within groundwaters, many of which involve the detection of crustacea, a dominant stygofauna taxa. Additional research on primers, the fate and transportation of DNA within aquifers and research on stygofauna DNA shedding capacity (Korbel, Rutlidge, et al, 2022; Trimbos et al, 2021) is required before this method can replace traditional sampling (Korbel, McKnight, et al, 2022; Saccò, Guzik, Van der Heyde, et al, 2022).…”

Section: Sampling Groundwater Faunamentioning

confidence: 99%

Global overview on groundwater fauna

Koch,

Blum,

Korbel

et al. 2023

Ecohydrology

View full text Add to dashboard Cite

Groundwater is an important global resource, providing water for irrigation, industry, geothermal uses and potable water. Moreover, groundwater contains the world's largest terrestrial freshwater biome with ecosystems, inhabited mainly by invertebrates (stygofauna) and microbes, undertaking important services including water purification, as well as nutrient and carbon cycling. Despite investigations on the spatial and temporal variations of groundwater fauna and the influence of environmental parameters on these organisms, in parts of the world, even the most basic knowledge of these ecosystems is still lacking. The aims of this study are to provide an overview on groundwater fauna (stygofauna) research, including the historical evolution of research topics and the development of sampling methods and secondly to identify the global distribution of groundwater fauna research and resulting data gaps. To achieve this, an extensive review of accessible groundwater fauna data was conducted by analysing 859 studies. It was evident that over time, there has been an exponential increase in the number of groundwater fauna studies together with changing paradigms in the research focus, particularly as sampling methods have developed from using simple nets, substrate samples and hand‐pumps in the beginning to recent molecular analyses (e.g. eDNA). As application of molecular methods becomes more common, knowledge on groundwater diversity and functional ecology is expected to increase. Studies on groundwater fauna are spatially uneven and are dominated by research in Europe and Australia, with few studies in Africa, Asia and the Americas. This presently biased view on groundwater biota hinders the identification of biodiversity patterns and ecosystem functions on a wider geographic and climatic scale. In the future, a more evenly distributed stygofauna sampling effort in currently underrepresented areas of the globe is necessary to ensure a more comprehensive perspective on stygofauna biodiversity, roles and functional significances. This is increasingly important with the accumulating knowledge of the sensitivities of these ecosystems to anthropogenic activities, including climate change, and is fundamental to effective management of these ecosystems.

show abstract

Section: Sampling Groundwater Faunamentioning

confidence: 99%

Global overview on groundwater fauna

Koch,

Blum,

Korbel

et al. 2023

Ecohydrology

View full text Add to dashboard Cite

show abstract

“…Unlike the conventional quantitative PCR (qPCR), ddPCR has a higher reproducibility, is generally less sensitive to inhibitors, and does not require calibration curves or high replicate counts (Doi et al, 2015;Hindson et al, 2013;Nathan et al, 2014;Yang et al, 2014). The protocol for quantification of F:B ratio by ddPCR is inspired by work from Trimbos et al (2021) and is described in Appendix A. In addition to the ratio of fungal to bacterial DNA concentrations, the sum of both DNA concentrations was taken as a second indicator for total microbial abundance.…”

Section: Amendment Characterizationmentioning

confidence: 99%

Relationships of priming effects with organic amendment composition and soil microbial properties

et al. 2022

Self Cite

View full text Add to dashboard Cite

“…Environmental DNA (eDNA) is a promising alternative to physical collection and processing [22][23][24]. The focus of species-specific crustacean eDNA assays using real-time quantitative polymerase chain reactions (rt-qPCR, henceforth qPCR) has often targeted rare or introduced species rather than abundant indicator species [25,26]. Water column eDNA may not allow for explicit crustacean quantification because much arthropod eDNA shedding may relate to molting processes that result in DNA deposition on or in the sediment [26][27][28].…”

Section: Introductionmentioning

confidence: 99%

Comparing Physical Collection and Environmental DNA Methods for Determining Abundance Patterns of Gammarus Species along an Estuarine Gradient

et al. 2023

View full text Add to dashboard Cite

Estuaries are productive systems with rapid changes in natural stressors, such as salinity, that make perturbation detection challenging. Amphipods are vital to estuarine assemblages and may serve as anthropogenic stress indicators. However, practical methods of monitoring species composition and abundance are lacking. This study aims to describe the spatial patterns of four Gammarus spp. in northwest Atlantic estuaries and to compare their compositions and abundances between collection methods using artificial substrates, macrophyte raking, light-baited traps, and species-specific quantitative PCR analyses from sediment environmental DNA (eDNA). Sampling occurred in upper, mid, and lower estuary zones within three estuaries of Prince Edward Island (Canada). G. tigrinus was rarely found in the upper zones with any method. G. mucronatus was predominant in the upper–mid zones across the physical methods, and its abundance declined with increasing salinity. G. lawrencianus was a dominant species across zones, but its abundance did not change with salinity. G. oceanicus was predominant in lower-zone artificial substrates. Species abundances generally correlated with physical collection methods. Sediment eDNA did not detect the spatial effects observed via the physical methods but was correlated with the mean counts of G. mucronatus. The Gammarus spp. assemblages are spatially partitioned in short estuaries, though the sampling method is critical when interpreting estuary patterns. Though multiple methods are ideal for compositional comparisons, abundance monitoring should employ light traps.

show abstract

Stirring up the relationship between quantified environmental DNA concentrations and exoskeleton‐shedding invertebrate densities

Abstract: This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Cited by 7 publications

References 88 publications

Global overview on groundwater fauna

Global overview on groundwater fauna

Relationships of priming effects with organic amendment composition and soil microbial properties

Comparing Physical Collection and Environmental DNA Methods for Determining Abundance Patterns of Gammarus Species along an Estuarine Gradient

Contact Info

Product

Resources

About