Evaluation of eDNA for groundwater invertebrate detection and monitoring: a case study with endangered Stygobromus (Amphipoda: Crangonyctidae)

Niemiller, Matthew L.; Porter, Megan L.; Keany, Jenna; Gilbert, Heather; Fong, Daniel W.; Culver, David C.; Hobson, Christopher S.; Kendall, K. Denise; Davis, Mark A.; Taylor, Steven J.

doi:10.1007/s12686-017-0785-2

Cited by 67 publications

(50 citation statements)

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“…For this, we recommend beginning with a tissue protocol lysis, adjusting the volumes as required, then following the water protocol from inhibitor removal through to elution. In this way, contaminants are greatly reduced and there is no need for extra purification of extractions (unlike with Niemiller et al 2017). However we found that neither DNeasy Blood and Tissue nor the adapted Mu-DNA: Tissue/Water protocol could achieve inhibition-free DNA from turbid, algal rich waters (Water B) as effectively as DNeasy PowerWater or Mu-DNA: Water (data not shown).…”

Section: Adaptability Of Mu-dnamentioning

confidence: 99%

“…DNeasy PowerSoil, or aspects thereof, has been used for stomach, gut or faecal analysis of invertebrates (Knapp et al 2010, O'Rorke et al 2015, fish (Koinari et al 2013, Bolnick et al 2014, reptiles (Lau et al 2013, Colston et al 2015, birds (Vo andJedlicka 2014, Lewis et al 2016), mammals (Parfrey et al 2014, Ishaq andWright 2014) and, in particular, the Human Microbiome Project (Aagaard et al 2013). DNeasy Blood and Tissue has been used for studies of environmental DNA (eDNA) from water samples (Rees et al 2014, Spens et al 2016, Niemiller et al 2017. Although widely used, commercial kits are expensive and separate kits can be required for different sample types.…”

Section: Introductionmentioning

confidence: 99%

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Mu-DNA: a modular universal DNA extraction method adaptable for a wide range of sample types

Sellers¹,

Muri²,

Gómez³

et al. 2018

MBMG

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Efficient DNA extraction is fundamental to molecular studies. However, commercial kits are expensive when a large number of samples need to be processed. Here we present a simple, modular and adaptable DNA extraction 'toolkit' for the isolation of high purity DNA from multiple sample types (modular universal DNA extraction method or Mu-DNA). We compare the performance of our method to that of widely used commercial kits across a range of soil, stool, tissue and water samples. Mu-DNA produced DNA extractions of similar or higher yield and purity to that of the commercial kits. As a proof of principle, we carried out replicate fish metabarcoding of aquatic eDNA extractions, which confirmed that the species detection efficiency of our method is similar to that of the most frequently used commercial kit. Our results demonstrate the reliability of Mu-DNA along with its modular adaptability to challenging sample types and sample collection methods. Mu-DNA can substantially reduce the costs and increase the scope of experiments in molecular studies.

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Section: Adaptability Of Mu-dnamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Mu-DNA: a modular universal DNA extraction method adaptable for a wide range of sample types

Sellers¹,

Muri²,

Gómez³

et al. 2018

MBMG

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show abstract

“…Thus, given that only a fraction of the habitat available to the species interacting within the biological community can be directly investigated, the results obtained should be relativized accordingly. More recently, the use of indirect molecular evidence for the presence of the species (environmental DNA) was also discussed (Gorički et al 2017, Vörös et al 2017, Niemiller et al 2018. Alternatively, this disadvantage can be overcome by using specific sampling devices for collecting the fauna inhabiting the network of fissure, whether air-filled (Mammola et al 2016a), temporarily water-filled (Ortuño et al 2013) or constantly water-filled (Brancelj 2004).…”

Section: Generalitiesmentioning

confidence: 99%

“…The use of such sampling tools has proven to provide a reliable means to characterise subterranean communities, especially if implemented in properly executed experimental protocols involving a wide spatial and/or temporal scale of investigation , Rendoš et al 2012, Ortuño et al 2013, Halse and Pearson 2014, Nitzu et al 2014, Jiménez-Valverde et al 2015, Mammola et al 2018a). More recently, the use of indirect molecular evidence for the presence of the species (environmental DNA) was also discussed (Gorički et al 2017, Vörös et al 2017, Niemiller et al 2018.…”

Section: Generalitiesmentioning

confidence: 99%

Finding answers in the dark: caves as models in ecology fifty years after Poulson and White

2018

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The use of semi-isolated habitats such as oceanic islands, lakes and mountain summits as model systems has played a crucial role in the development of evolutionary and ecological theory. Soon after the discovery of life in caves, different pioneering authors similarly recognized the great potential of these peculiar habitats as biological model systems. In their 1969 paper in Science, 'The cave environment', Poulson and White discussed how caves can be used as natural laboratories in which to study the underlying principles governing the dynamics of more complex environments. Together with other seminal syntheses published at the time, this work contributed to establishing the conceptual foundation for expanding the scope and relevance of cave-based studies. Fifty years after, the aim of this review is to show why and how caves and other subterranean habitats can be used as eco-evolutionary laboratories. Recent advances and directions in different areas are provided, encompassing community ecology, trophicwebs and ecological networks, conservation biology, macroecology and climate change biology. Special emphasis is given to discuss how caves are only part of the extended network of fissures and cracks that permeate most substrates and, thus, their ecological role as habitat islands is critically discussed. Numerous studies have quantified the relative contribution of abiotic, biotic and historical factors in driving species distributions and community turnovers in space and time, from local to regional scales. Conversely, knowledge of macroecological patterns of subterranean organisms at a global scale remains largely elusive, due to major geographical and taxonomical biases. Also, knowledge regarding subterranean trophic webs and the effect of anthropogenic climate change on deep subterranean ecosystems is still limited. In these research fields, the extensive use of novel molecular and statistical tools may hold promise for quickly producing relevant information not accessible hitherto.

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“…For example, this issue is especially serious in regions where subterranean biology has only recently started to grow, such as the Neotropics (Trajano and Bichuette 2009, Silva and Ferreira 2016, Trajano et al 2016. Incidentally, the distribution of most taxa is expect to be underestimated even in areas with historical and consolidated speleobiological traditions (Zagmajster et al 2008(Zagmajster et al , 2010) -although the use of modern surveillance tools, such as environmental DNA, is recently helping to overcome this impediment (Gorički et al 2017, Năpăruș-Aljančič et al 2017, Niemiller et al 2017, Vörös et al 2017.…”

Section: Sampling Biasesmentioning

confidence: 99%

Applying species distribution models to caves and other subterranean habitats

Mammola¹,

Leroy

2017

Ecography

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Over the last two decades there has been an exponential increase in the use of correlative species distribution models (SDMs) to address a variety of topics in ecology, biogeography, evolution, and conservation biology. Conversely, the use of these statistical methods to study the potential distribution of subterranean organisms has lagged behind, relative to their above‐ground (epigean) counterparts. The reason for this is possibly related to a number of peculiarities of subterranean systems, which pose important limits, but also opportunities, for these correlative models. The aim of this forum is to explore the caveats that need to be made when generalizing these statistical techniques to caves and other subterranean habitats. We focus on the typical bias in spatial datasets of cave‐dwelling species, and provide advice for selecting the model calibration area. In parallel, we discuss the potential use of different large scale surface variables to represent the subterranean condition. A more widespread adoption of these statistical techniques in subterranean biology is highly attractive and has great potential in broadening our knowledge on a variety of ecological topics, especially in the fields of climate change and biodiversity conservation. Their use would especially benefit the study of the biogeographic patterns of subterranean fauna and the impact of past and future climate change on subterranean ecosystems.

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Evaluation of eDNA for groundwater invertebrate detection and monitoring: a case study with endangered Stygobromus (Amphipoda: Crangonyctidae)

Cited by 67 publications

References 50 publications

Mu-DNA: a modular universal DNA extraction method adaptable for a wide range of sample types

Mu-DNA: a modular universal DNA extraction method adaptable for a wide range of sample types

Finding answers in the dark: caves as models in ecology fifty years after Poulson and White

Applying species distribution models to caves and other subterranean habitats

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