• Combining ddPCR and environmental DNA to improve detection capabilities of a critically endangered freshwater invertebrate

      Mauvisseau, Quentin; Davy-Bowker, John; Bulling, Mark; Brys, Rein; Neyrinck, Sabrina; Troth, Christopher; Sweet, Michael; University of Derby; Freshwater Biological Association, Dorset; Natural History Museum, London; et al. (Springer Science and Business Media LLC, 2019-10-01)
      Isogenus nubecula is a critically endangered Plecoptera species. Considered extinct in the UK, I. nubecula was recently rediscovered (in one location of the River Dee, Wales), after 22 years of absence. In a similar way to many other species of Perlodidae, I. nubecula could be utilised as a bio-indicator, for assessing water quality and health status of a given freshwater system. However, conventional monitoring of invertebrates via kick-sampling, is invasive and expensive (time consuming). Further, such methods require a high level of taxonomic expertise. Here, we compared the traditional kick-sampling method with the use of eDNA detection using qPCR and ddPCR-analyses. In spring 2018, we sampled eDNA from twelve locations on the River Dee. I. nubecula was detected using kick-sampling in five of these locations, three locations using both eDNA detection and kick-sampling and one location using eDNA detection alone – resulting in a total of six known and distinct populations of this critically endangered species. Interestingly, despite the eDNA assay being validated in vitro and in silico, and results indicating high sensitivity, qPCR analysis of the eDNA samples proved to be ineffective. In contrast, ddPCR analyses resulted in a clear detection of I. nubecula at four locations suggesting that inhibition most likely explains the large discrepancy between the obtained qPCR and ddPCR results. It is therefore important to explore inhibition effects on any new eDNA assay. We also highlight that ddPCR may well be the best option for the detection of aquatic organisms which are either rare or likely to shed low levels of eDNA into their environment.
    • Mineralogical and geochemical characterisation of warm-water, shallow-marine glaucony from the Tertiary of the London Basin

      Huggett, Jennifer; Adetunji, Jacob; Longstaffe, Fred; Wray, David; Natural History Museum, London; University of Derby; University of Western Ontario; University of Greenwich (Mineralogical Society, 2017-11-27)
      Glaucony is present in the Palaeocene sediments of the London Basin, from the Thanet Sand Formation to the gravel beds at the base of the Lower Mottled Beds of the Reading Formation. The Upnor Formation glaucony is a rare example of formation in warm, shallow, brackish water and this, combined with the ready availability of fresh material from boreholes, make this study important in developing our understanding of this mineral. Glaucony comprises up to 50% of the Upnor Formation, a grey to green sandstone, of variable thickness and composition, which was deposited in a warm, shallow, marine to estuarine environment, ∼55.6–56.2 Ma. Using morphological criteria, X-ray diffraction data and K+ abundance, the Upnor glaucony may be defined as evolved. The underlying shallow marine Thanet Sand contains <5% of nascent to slightly evolved glaucony. The rare earth element (REE) data for the Upnor Formation suggest more than one source for the sediment from which the Upnor glaucony formed, while the Thanet REE data are consistent with a large detrital clay component. In the Upnor Formation, the large proportion of glaucony that occurs as granule fragments rather than whole granules, and the high-energy estuarine to shallow-marine environment of deposition, are indicative of reworking. The Upnor glaucony is inferred to be intraformationally reworked, rather than derived from the Thanet Sand Formation. The glaucony may have formed in sediments deposited away from the main estuarine channel, and been subsequently reworked into higher-energy sediments. Warm seas with freshwater mixing are more typically characteristic of verdine formation than of glaucony. The shallow, brackish environment of deposition suggests that there is not a clear distinction between the environmental requirements of verdine (or odinite) and glaucony (or glauconite), as is often proposed. The highly fractured, delicate nature of some granules indicates that they have experienced some maturation in situ, after reworking. The oxygen and hydrogen isotopic compositions of Upnor Formation shark teeth and glaucony point to formation in low-salinity water at ∼23 ± 3°C, also consistent with formation in the Upnor Formation, rather than in a fully marine sediment and subsequent reworking. A higher than normal temperature of formation may have increased the rate of evolution of glaucony. Our multidisciplinary study considers many of the factors relating to depositional environment that must be considered when glaucony-rich facies are encountered in comparable palaeo-environmental settings elsewhere in the geological record.