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

Context Translocations are becoming an increasingly important conservation tool to combat rising levels of species extinction. Unfortunately, many translocation efforts fail; yet, the timing and cause of failure often remain unknown. Monitoring individuals in the days and weeks following release can provide valuable information on their capacity to survive this initial hurdle. In Australia, breeding programs have been established for the endangered northern corroboree frog, Pseudophryne pengilleyi, to enable reintroduction to the wild via captive-reared individuals, typically, early life stages such as eggs or juvenile frogs that cannot be monitored via traditional survey methods that target adult frogs (e.g. shout–response). Environmental DNA (eDNA) detects trace amounts of DNA that organisms release into their environment and could provide a means to infer population persistence for wildlife releases and translocations. Aims In the present study, we aim to develop an eDNA assay capable of detecting both sexes of P. pengilleyi across multiple life stages, and use it to monitor their survival. Methods An eDNA assay was developed to target the two corroboree frog species (P. pengilleyi and P. corroboree, the southern corroboree frog) and was tested for its sensitivity and specificity in silico and in vitro. Pseudophryne pengilleyi eggs were released into three naturally occurring ponds and water samples were, subsequently, collected from each pond on several occasions over a period of 78 days. Quantitative polymerase chain reaction was used to detect P. pengilleyi eDNA from water samples. Key Results The developed assay was shown to be sensitive and specific to corroboree frogs. eDNA monitoring of reintroduced P. pengilleyi detected the species’ DNA at three of three release ponds and DNA remained detectable until at least 78 days post-release at two of three ponds. Conclusions We show how the development of a corroboree frog-specific assay allowed us to monitor the post-release survival of P. pengilleyi in naturally occurring pools. Implications eDNA surveys may provide a useful tool to monitor post-release survival of translocated populations in a non-invasive manner, with the potential to identify the timing and causes of failure. Such knowledge can be used to inform the management of translocated populations and future release strategies.

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Microplastics in the gastrointestinal tracts of fish and the water from an urban prairie creek

FACETS ◽

10.1139/facets-2017-0008 ◽

2017 ◽

Vol 2 (1) ◽

pp. 395-409 ◽

Cited By ~ 47

Author(s):

Samantha H. Campbell ◽

Patrick R. Williamson ◽

Britt D. Hall

Keyword(s):

Wastewater Treatment ◽

Wastewater Treatment Plant ◽

Water Samples ◽

Treatment Plant ◽

Aquatic Organisms ◽

Creek Water ◽

Treated Effluent ◽

Baseline Conditions ◽

Freshwater Environments

Microplastics are defined as any plastic with a diameter ≤5 mm. Problems associated with these plastics such as contamination of both marine and freshwater environments and ingestion by aquatic organisms are of increasing concern. Our study quantifies the number of microplastics in a prairie creek immediately downstream of Regina, Saskatchewan, Canada. Water samples and five species of fish were collected from sample sites upstream and downstream of a wastewater treatment plant (WWTP) in the summers of 2015 and 2016. Samples were digested in either a Fe(II)/H2O2 or NaClO solution and observed under a microscope where plastics present were enumerated by colour and type. At least one microplastic was detected in 73.5% of fish and 95.6% of water samples, showing that the creek does, in fact, contain microplastics. Concentrations were higher in water from upstream sites, likely due to dilution of creek water by the release of treated effluent. The results of this study provide baseline conditions for the presence of plastics in the creek prior to a major upgrade of the WWTP scheduled for completion in 2016.

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Development of an environmental DNA method for monitoring fish communities: ground truthing in diverse lakes with characterised fish faunas

10.1101/394718 ◽

2018 ◽

Author(s):

Jianlong Li ◽

Tristan W. Hatton-Ellis ◽

Lori-Jayne Lawson Handley ◽

Helen S. Kimbell ◽

Marco Benucci ◽

...

Keyword(s):

Water Samples ◽

Fish Communities ◽

Environmental Dna ◽

Quantitative Information ◽

12S Rrna ◽

Similar Species ◽

List Type ◽

Large Lakes ◽

Non Invasive ◽

Wide Range

AbstractAccurate, cost-effective monitoring of fish is required to assess the quality of lakes under the European Water Framework Directive (WFD). Recent studies have shown that environmental DNA (eDNA) metabarcoding is an effective and non-invasive method, which can provide semi-quantitative information on fish communities in large lakes.This study further investigated the potential of eDNA metabarcoding as a tool for WFD status assessment by collecting and analysing water samples from eight Welsh lakes and six meres in Cheshire, England, with well described fish faunas. Water samples (N = 252) were assayed using two mitochondrial DNA regions (Cytb and 12S rRNA).eDNA sampling indicated the presence of very similar species in the lakes compared to those expected on the basis of existing and historical information. In total, 24 species were detected with a total of 111 species occurrences in the lakes studied using eDNA. Secondly, there was a significant positive correlation between expected faunas and eDNA data in terms of confidence of species occurrence (Spearman’s r = 0.74, df = 109, p <; 0.001). Thirdly, eDNA data can estimate relative abundance with the standard five-level classification scale (“DAFOR”). Lastly, four ecological fish communities were characterised using eDNA data which agrees with the pre-defined lake types according to environmental characteristics.Synthesis and applications. This study provides further evidence that eDNA metabarcoding could be a powerful and non-invasive monitoring tool for WFD purpose in a wide range of lake types, considerably outperforming other methods for community level analysis.

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Pollutant Identification by Selected Area Electron Diffraction

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100052675 ◽

1974 ◽

Vol 32 ◽

pp. 532-533

Author(s):

R. E. Ferrell ◽

G. G. Paulson ◽

C. W. Walker

Keyword(s):

Thermal Treatment ◽

Electron Diffraction ◽

Sample Preparation ◽

Crystal Structures ◽

Water Samples ◽

Environmental Samples ◽

Short Review ◽

Selected Area Electron Diffraction ◽

Multiple Component

Selected area electron diffraction (SAD) has been used successfully to determine crystal structures, identify traces of minerals in rocks, and characterize the phases formed during thermal treatment of micron-sized particles. There is an increased interest in the method because it has the potential capability of identifying micron-sized pollutants in air and water samples. This paper is a short review of the theory behind SAD and a discussion of the sample preparation employed for the analysis of multiple component environmental samples.

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Enumeration and Identification of Asbestos Fibres in Water

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010005264x ◽

1974 ◽

Vol 32 ◽

pp. 526-527 ◽

Cited By ~ 1

Author(s):

O. Mudroch ◽

J. R. Kramer

Keyword(s):

Water Supply ◽

Water Samples ◽

Drainage Basin ◽

Lake Superior ◽

Research Work ◽

List Type ◽

The West ◽

Asbestos Fibre ◽

Amphibole Asbestos

Approximately 60,000 tons per day of waste from taconite mining, tailing, are added to the west arm of Lake Superior at Silver Bay. Tailings contain nearly the same amount of quartz and amphibole asbestos, cummingtonite and actinolite in fibrous form. Cummingtonite fibres from 0.01μm in length have been found in the water supply for Minnesota municipalities.The purpose of the research work was to develop a method for asbestos fibre counts and identification in water and apply it for the enumeration of fibres in water samples collected(a) at various stations in Lake Superior at two depth: lm and at the bottom.(b) from various rivers in Lake Superior Drainage Basin.

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X-ray microtomography

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100107058 ◽

1988 ◽

Vol 46 ◽

pp. 998-999

Author(s):

H.W. Deckman ◽

B.F. Flannery ◽

J.H. Dunsmuir ◽

K.D' Amico

Keyword(s):

Computed Tomography ◽

Internal Structure ◽

Imaging Technique ◽

Three Dimensional ◽

Tissue Structure ◽

Individual Element ◽

X Ray ◽

Non Invasive ◽

Panoramic Imaging ◽

Three Dimensional Images

We have developed a new X-ray microscope which produces complete three dimensional images of samples. The microscope operates by performing X-ray tomography with unprecedented resolution. Tomography is a non-invasive imaging technique that creates maps of the internal structure of samples from measurement of the attenuation of penetrating radiation. As conventionally practiced in medical Computed Tomography (CT), radiologists produce maps of bone and tissue structure in several planar sections that reveal features with 1mm resolution and 1% contrast. Microtomography extends the capability of CT in several ways. First, the resolution which approaches one micron, is one thousand times higher than that of the medical CT. Second, our approach acquires and analyses the data in a panoramic imaging format that directly produces three-dimensional maps in a series of contiguous stacked planes. Typical maps available today consist of three hundred planar sections each containing 512x512 pixels. Finally, and perhaps of most import scientifically, microtomography using a synchrotron X-ray source, allows us to generate maps of individual element.

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Stabilizing pyritic material

The Paleontological Society Special Publications ◽

10.1017/s2475262200005207 ◽

1989 ◽

Vol 4 ◽

pp. 244-248 ◽

Cited By ~ 2

Author(s):

Donald L. Wolberg

Keyword(s):

Significant Contribution ◽

Organic Materials ◽

Sedimentary Rocks ◽

Iron Sulfides ◽

Decomposition Products ◽

Iron Minerals ◽

Pyrite Formation ◽

Organic Sediments ◽

Freshwater Environments

The minerals pyrite and marcasite (broadly termed pyritic minerals) are iron sulfides that are common if not ubiquitous in sedimentary rocks, especially in association with organic materials (Berner, 1970). In most marine sedimentary associations, pyrite and marcasite are associated with organic sediments rich in dissolved sulfate and iron minerals. Because of the rapid consumption of sulfate in freshwater environments, however, pyrite formation is more restricted in nonmarine sediments (Berner, 1983). The origin of the sulfur in nonmarine environments must lie within pre-existing rocks or volcanic detritus; a relatively small, but significant contribution may derive from plant and animal decomposition products.

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