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"Power, Matthew"
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Development and evaluation of fish eDNA metabarcoding assays facilitate the detection of cryptic seahorse taxa (family: Syngnathidae)
Environmental DNA (eDNA) metabarcoding methods have demonstrated their potential as noninvasive techniques for the monitoring and conservation of marine fishes, including rare and endangered taxa. However, the majority of these investigations have focused on large‐bodied taxa such as sharks and sturgeons. In contrast, eDNA studies on small‐bodied cryptic taxa are much less common. As a case in point, seahorses (members of the Syngnathidae family) have never been detected by eDNA, despite the fact that globally there are 14 species classified as “Threatened” by the IUCN. Here, we critically evaluate the ability of two existing broad‐spectrum fish metabarcoding assays (MiFish and 16S Fish) and explore the efficacy of two newly designed fish metabarcoding assays (16S_FishSyn_Short and 16S_FishSyn_Long) to detect Syngnathidae amidst a wide spectrum of fish species. Furthermore, a custom Western Australian 16S rRNA fish database was created to increase the likelihood of correct taxonomic assignments. With the newly designed assays, we detected four Syngnathidae species in a targeted eDNA survey of the Perth metropolitan area (Western Australia). These detections include the seahorse species Hippocampus subelongatus and Hippocampus breviceps, which represents the first time seahorse species have been detected using eDNA. The existing MiFish and 16S Fish assays did not detect any Syngnathidae. This evaluation of all four fish metabarcoding assays reinforces the view that every PCR assay has “blind spots”. In the context of complex environmental samples, no assay is universal and false negatives will occur due to a combination of PCR efficacy, primer binding, assay sensitivity, degeneracies in the primers, template competition, and amplicon length. Taken together, these data indicate that eDNA methodologies, with ongoing optimizations, will become an integral part of monitoring small‐bodied cryptic taxa such as seahorses, gobies, and blennies and can assist in mapping species’ distributions and prioritizing conservation areas.
Journal Article
لماذا ننام : اكتشف طاقة النوم والأحلام
جولة ذكية في ميدان النوم الذي لا يزال فهمنا له غامضا ... كتاب وضع لنفسه مهمة محددة ووكر واقع في غرام النوم، ويريدنا أن نقع في غرامه مثله والأمر لا يحتمل التأجيل يقيم ووكر الحجة المقنعة على أننا مصابون \"بوباء نقص النوم الذي يفتك بنا صامتا\" ويمثل أكبر تحد نواجهه في عصرنا ... يدافع هذا الكتاب عن وجوب معالجة نقص النوم الذي نعانيه وعن حسنات النوم كتاب يستحق أن يوضع إلى جانب السرير من أجل القراءة قبل النوم\".
Book
Maximizing fish detection with eDNA metabarcoding
Fish biodiversity can be measured by capturing and then sequencing free DNA present in water. Such environmental DNA (eDNA) methods offer an effective, noninvasive tool for species diversity measurement, although standardized protocols are not yet developed. We investigate how metrics of fish biodiversity revealed through eDNA analysis of water are influenced by sampling volume. Water samples were collected from the intertidal reef of Browse Island, a tropical, remote island in the Timor Sea. Aliquots from a single 20,700‐ml sample and multiple 2,000‐ml samples were filtered in various volumes (25–2,000 ml) across two membrane sizes (0.20 and 0.45 µm). A fish metabarcoding assay was used to characterize the fish diversity within aliquots. All samples, except one, yielded fish DNA sequences. Two hundred and nine operational taxonomic units (cf. species) representing 48 fish families were identified from the complete collection of DNA contained in all samples, comparable to the 200 fish species detected using conventional surveys at this location. Notable additions from eDNA methods were cryptic and nocturnal fish species. Nevertheless, large differences in taxonomic composition (<60% species overlap) between aliquots of identical volumes demonstrate that eDNA in seawater is patchy and that estimates of biodiversity are strongly influenced by the volume of water filtered. We suggest that eDNA studies maximize water volumes as much as logistically possible if the aim is to detect the greatest number of taxa and that species accumulation curves be provided as an indication of sampling adequacy. We investigate how metrics of fish biodiversity revealed through eDNA analysis of water are influenced by sampling volume. We demonstrate that eDNA in seawater is patchy and that estimates of biodiversity are strongly influenced by the volume of water filtered. We suggest that eDNA studies maximize water volumes as much as logistically possible if the aim is to detect the greatest number of taxa, and that species accumulation curves be provided as an indication of sampling adequacy.
Journal Article
لماذا ننام : اكتشف طاقة النوم والأحلام
جولة ذكية في ميدان النوم الذي لا يزال فهمنا له غامضا ... كتاب وضع لنفسه مهمة محددة ووكر واقع في غرام النوم، ويريدنا أن نقع في غرامه مثله والأمر لا يحتمل التأجيل يقيم ووكر الحجة المقنعة على أننا مصابون \"بوباء نقص النوم الذي يفتك بنا صامتا\" ويمثل أكبر تحد نواجهه في عصرنا ... يدافع هذا الكتاب عن وجوب معالجة نقص النوم الذي نعانيه وعن حسنات النوم كتاب يستحق أن يوضع إلى جانب السرير من أجل القراءة قبل النوم\".
Book
Petrological and geochemical characterisation of the sarsen stones at Stonehenge
Little is known of the properties of the sarsen stones (or silcretes) that comprise the main architecture of Stonehenge. The only studies of rock struck from the monument date from the 19 th century, while 20 th century investigations have focussed on excavated debris without demonstrating a link to specific megaliths. Here, we present the first comprehensive analysis of sarsen samples taken directly from a Stonehenge megalith (Stone 58, in the centrally placed trilithon horseshoe). We apply state-of-the-art petrographic, mineralogical and geochemical techniques to two cores drilled from the stone during conservation work in 1958. Petrographic analyses demonstrate that Stone 58 is a highly indurated, grain-supported, structureless and texturally mature groundwater silcrete, comprising fine-to-medium grained quartz sand cemented by optically-continuous syntaxial quartz overgrowths. In addition to detrital quartz, trace quantities of silica-rich rock fragments, Fe-oxides/hydroxides and other minerals are present. Cathodoluminescence analyses show that the quartz cement developed as an initial <10 μm thick zone of non-luminescing quartz followed by ~16 separate quartz cement growth zones. Late-stage Fe-oxides/hydroxides and Ti-oxides line and/or infill some pores. Automated mineralogical analyses indicate that the sarsen preserves 7.2 to 9.2 area % porosity as a moderately-connected intergranular network. Geochemical data show that the sarsen is chemically pure, comprising 99.7 wt. % SiO 2 . The major and trace element chemistry is highly consistent within the stone, with the only magnitude variations being observed in Fe content. Non-quartz accessory minerals within the silcrete host sediments impart a trace element signature distinct from standard sedimentary and other crustal materials. 143 Nd/ 144 Nd isotope analyses suggest that these host sediments were likely derived from eroded Mesozoic rocks, and that these Mesozoic rocks incorporated much older Mesoproterozoic material. The chemistry of Stone 58 has been identified recently as representative of 50 of the 52 remaining sarsens at Stonehenge. These results are therefore representative of the main stone type used to build what is arguably the most important Late Neolithic monument in Europe.
Journal Article
Phase Characterisation for Recycling of Shredded Waste Printed Circuit Boards
In this study, we adopt a geometallurgical analytical approach common in mineral processing in the characterization of samples of shredded waste printed circuit board (PCB) E-waste, originating from Europe. Conventionally, bulk chemical analysis provides a value for E-waste; however, chemical analysis alone does not provide information on the textural variability, phase complexity, grain size, particle morphology, phase liberation and associations. To address this, we have integrated analysis using binocular microscopy, manual scanning electron microscopy, phase, textural and compositional analyses by automated (SEM-EDS), phase analysis based on (Automated Material Identification and Classification System (AMICS) software, and elemental analysis using micro-XRF. All methods used have strengths and limitations, but an integration of these analytical tools allows the detailed characterization of the texture and composition of the E-waste feeds, ahead of waste reprocessing. These data can then be used to aid the design of optimized processing circuits for the recovery of the key payable components, and assist in the commercial trading of e-scrap.
Journal Article
Evidence for fungi and gold redox interaction under Earth surface conditions
Microbial contribution to gold biogeochemical cycling has been proposed. However, studies have focused primarily on the influence of prokaryotes on gold reduction and precipitation through a detoxification-oriented mechanism. Here we show, fungi, a major driver of mineral bioweathering, can initiate gold oxidation under Earth surface conditions, which is of significance for dissolved gold species formation and distribution. Presence of the gold-oxidizing fungus TA_pink1, an isolate of
Fusarium oxysporum
, suggests fungi have the potential to substantially impact gold biogeochemical cycling. Our data further reveal that indigenous fungal diversity positively correlates with in situ gold concentrations. Hypocreales, the order of the gold-oxidizing fungus, show the highest centrality in the fungal microbiome of the auriferous environment. Therefore, we argue that the redox interaction between fungi and gold is critical and should be considered in gold biogeochemical cycling.
The role of fungi in the biogeochemical cycling of gold remains unclear. Here the authors show that fungi can initiate gold oxidation under supergene conditions, thereby impacting gold mobilisation and secondary deposit formation in terrestrial environments.
Journal Article
The Recycling of End-of-Life Lithium-Ion Batteries and the Phase Characterisation of Black Mass
Black mass is the industry term applied to end-of-life (EoL) lithium-ion batteries that have been mechanically processed for potential use as a recycled material to recover the valuable metals present, including cobalt, lithium, manganese, nickel and copper. A significant challenge to the effective processing of black mass is the complexity of the feed material. Two samples of black mass from a European source were analysed using a combination of methods including automated SEM-EDS (AMICS) to characterise and quantify the phases present and particle chemistry. Micro X-CT imaging, overlain onto automated mineralogy images, enabled the 3D morphology of the particles to be determined. Micro-XRF was used to map the copper, nickel, manganese and cobalt-bearing phases. Since Li cannot be detected using SEM-EDS, its abundance was semi-quantified using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). The integration of these complimentary analytical methods allowed for detailed phase characterisation, which may guide the potential hydrometallurgical or pyrometallurgical recycling routes and chemical assaying.
Journal Article
Environmental DNA reveals a multi‐taxa biogeographic break across the Arabian Sea and Sea of Oman
Environmental DNA (eDNA) is increasingly being used to assess community composition in marine ecosystems. Applying eDNA approaches across broad spatial scales now provide the potential to inform biogeographic analyses. However, to date, few studies have employed this technique to assess broad biogeographic patterns across multiple taxonomic groups. Here, we compare eDNA‐derived communities of bony fishes and invertebrates, including corals and sponges, from 15 locations spanning the entire length of the Omani coast. This survey includes a variety of habitats, including coral and rocky reefs, and covers three distinct marine ecoregions. Our data support a known biogeographic break in fish communities between the north and the south of Oman; however, the eDNA data highlight that this faunal break is mostly reflected in schooling baitfish species (e.g., sardines and anchovies), whereas reef‐associated fish communities appear more homogeneous along this coastline. Furthermore, our data provide indications that these biogeographic breaks also affect invertebrate communities, which includes corals, sponges, and broader eukaryotic groups. The observed community shifts were correlated with local environmental and anthropogenic differences characteristic of this coastline, particularly for the eDNA‐derived bony fish communities. Overall, this study provides compelling support that eDNA sequencing and associated analyses may serve as powerful tools to detect community differences across biogeographic breaks and ecoregions, particularly in places where there is significant variation in oceanographic conditions or anthropogenic impacts. We conducted a multi‐marker eDNA metabarcoding survey across the coastline of Oman to assess whether eDNA‐derived fish and invertebrate communities reflected a biogeographic break between the north and the south of Oman. The eDNA data indicated that this faunal break is mostly reflected in schooling baitfish species but also included corals, sponges, and broader eukaryotic groups. The observed community shifts showed some correlation with local environmental and anthropogenic differences characteristic of this coastline, particularly for the eDNA‐derived fish communities.
Journal Article