• I am really ever so not good at graph drawing: the Charlie and Lola approach to lineweaver-burk plots

      Beaumont, Ellen S.; Wilkinson, Alan-Shaun; Derby University (The Chemical Educator, 2015-09)
      Marking exam scripts can be eye-opening to instructors in terms of identifying errors in their preconceptions of students’ data handling and graph drawing skills. This short communication reports a novel approach to reducing the errors of undergraduate Biological and Forensic Science students in graphical representation of enzyme kinetic data. The approach involves using fictional units, the names of which are drawn from a popular children’s animated television series. Increases of 30.8% and 25.9% were recorded in the marks awarded for correct axis labelling in an end of module exam when compared to the two previous cohorts, suggesting the approach may be worthy of further exploration.
    • Identification of a bacterial pathogen associated with Porites white patch syndrome in the Western Indian Ocean

      Séré, Mathieu G.; Chabanet, Pascale; Quod, Jean-Pascal; Sweet, Michael J.; Tortosa, Pablo; Schleyer, Michael; University of Derby; Agence pour la Recherche et la Valorisation Marines (ARVAM); Ste Clotilde Reunion Island France; Unité Mixte de Recherche “Processus Infectieux en Milieu Insulaire Tropical” (UMR PIMIT); Université de La Réunion; Inserm1187; CNRS9192, IRD249; Plateforme de Recherche CYROI; 2 rue Maxime Rivière 97490 Ste Clotilde Saint Denis France; IRD - UMR ENTROPIE; Labex CORAIL; CS 41095 97495 Sainte Clotilde Cedex La Réunion; et al. (Wiley, 2015-08-24)
      Porites white patch syndrome (PWPS) is a coral disease recently described in the Western Indian Ocean. This study aimed to isolate and identify potential pathogens associated with PWPS utilizing both culture and nonculture screening techniques and inoculation trials. A total of 14 bacterial strains (those dominant in disease lesions, absent or rare in healthy tissues and considered potential pathogens in a previous study) were cultured and used to experimentally inoculate otherwise healthy individuals in an attempt to fulfil Henle–Koch's postulates. However, only one (P180R), identified as closely related (99–100% sequence identity based on 1.4 kb 16S RNA sequence) to Vibrio tubiashii, elicited signs of disease in tank experiments. Following experimental infection (which resulted in a 90% infection rate), the pathogen was also successfully re-isolated from the diseased tissues and re-inoculated in healthy corals colonies, therefore fulfilling the final stages of Henle–Koch's postulates. Finally, we report that PWPS appears to be a temperature-dependent disease, with significantly higher tissue loss (anova: d.f. = 2, F = 39.77, P < 0.01) occurring at 30 °C [1.45 ± 0.85 cm2 per day (mean ± SE)] compared to ambient temperatures of 28 and 26 °C (0.73 ± 0.80 cm2 per day (mean ± SE) and 0.51 ± 0.50 cm2 per day (mean ± SE), respectively).
    • Identification of an arginine-rich motif in human papillomavirus type 1 E1^E4 protein necessary for E4-mediated inhibition of cellular DNA Synthesis In Vitro and in Cells

      Roberts, Sally; Kingsbury, S. R.; Stoeber, K.; Knight, Gillian L.; Gallimore, P. H.; Williams, Gareth H. (2013-03-20)
      Productive infections by human papillomaviruses (HPVs) are restricted to nondividing, differentiated keratinocytes. HPV early proteins E6 and E7 deregulate cell cycle progression and activate the host cell DNA replication machinery in these cells, changes essential for virus synthesis. Productive virus replication is accompanied by abundant expression of the HPV E4 protein. Expression of HPV1 E4 in cells is known to activate cell cycle checkpoints, inhibiting G2-to-M transition of the cell cycle and also suppressing entry of cells into S phase. We report here that the HPV1 E4 protein, in the presence of a soluble form of the replicationlicensing factor (RLF) Cdc6, inhibits initiation of cellular DNA replication in a mammalian cell-free DNA replication system. Chromatin-binding studies show that E4 blocks replication initiation in vitro by preventing loading of the RLFs Mcm2 and Mcm7 onto chromatin. HPV1 E4-mediated replication inhibition in vitro and suppression of entry of HPV1 E4-expressing cells into S phase are both abrogated upon alanine replacement of arginine 45 in the full-length E4 protein (E1^E4), implying that these two HPV1 E4 functions are linked. We hypothesize that HPV1 E4 inhibits competing host cell DNA synthesis in replication-activated suprabasal keratinocytes by suppressing licensing of cellular replication origins, thus modifying the phenotype of the infected cell in favor of viral genome amplification.
    • Identification of multi-style hydrothermal alteration using integrated compositional and topographic remote sensing datasets

      Ferrier, Graham; Naden, Jon; Ganas, Athanassios; Kemp, Simon; Pope, Richard J. J.; University of Hull; British Geological Survey; National Observatory of Athens; British Geological Survey; University of Derby (Multidisciplinary Digital Publishing Institute (MDPI), 2016-07-29)
      The western part of the island of Milos, Greece has undergone widespread, intense alteration associated with a range of mineralization, including seafloor Mn-Fe-Ba, sub seafloor Pb-Zn-Ag, and epithermal Au-Ag. The surrounding country rocks are a mixture of submarine and subaerial calc-alkaline volcanic rocks ranging from basaltic andesite to rhyolite in composition, but are predominantly andesites and dacites. The current surface spatial distribution of the alteration mineralogy is a function not only of the original hydrothermal, but also subsequent tectonic and erosional processes. The high relief and the excellent rock exposure provide ideal conditions to evaluate the potential of Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) satellite remote sensing data to identify and differentiate the different styles of alteration mineralisation. Laboratory spectral reflectance and calculated emittance measurements of field samples, supported by XRD analysis and field mapping, were used to support the analysis. Band ratio and spectral matching techniques were applied to the shortwave-infrared (SWIR) reflectance and thermal-infrared (TIR) emissivity imagery separately and were then integrated with topographic data. The band ratio and spectral matching approaches produced similar results in both the SWIR and TIR imagery. In the SWIR imagery, the advanced argillic, argillic and hydrous silica alteration zones were clearly identifiable, while in the TIR imagery, the silicic and advanced argillic alteration zones, along with the country rock, were differentiable. The integrated mineralogical–topographic datasets provided an enhanced understanding of the spatial and altitude distribution of the alteration zones when combined with conceptual models of their genesis, which provides a methodology for the differentiation of the multiple styles of alteration.
    • Impact of biodiversity-climate futures on primary production and metabolism in a model benthic estuarine system

      Hicks, Natalie; Bulling, Mark T.; Solan, Martin; Raffaelli, D.; White, Piran C. L.; Paterson, David M. (2013-05-24)
      Background: Understanding the effects of anthropogenically-driven changes in global temperature, atmospheric carbon dioxide and biodiversity on the functionality of marine ecosystems is crucial for predicting and managing the associated impacts. Coastal ecosystems are important sources of carbon (primary production) to shelf waters and play a vital role in global nutrient cycling. These systems are especially vulnerable to the effects of human activities and will be the first areas impacted by rising sea levels. Within these coastal ecosystems, microalgal assemblages (microphytobenthos: MPB) are vital for autochthonous carbon fixation. The level of in situ production by MPB mediates the net carbon cycling of transitional ecosystems between net heterotrophic or autotrophic metabolism. In this study, we examine the interactive effects of elevated atmospheric CO 2 concentrations (370, 600, and 1000 ppmv), temperature (6°C, 12°C, and 18°C) and invertebrate biodiversity on MPB biomass in experimental systems. We assembled communities of three common grazing invertebrates ( Hydrobia ulvae, Corophium volutator and Hediste diversicolor) in monoculture and in all possible multispecies combinations. This experimental design specifically addresses interactions between the selected climate change variables and any ecological consequences caused by changes in species composition or richness. Results: The effects of elevated CO 2 concentration, temperature and invertebrate diversity were not additive, rather they interacted to determine MPB biomass, and overall this effect was negative. Diversity effects were underpinned by strong species composition effects, illustrating the importance of individual species identity. Conclusions: Overall, our findings suggest that in natural systems, the complex interactions between changing environmental conditions and any associated changes in invertebrate assemblage structure are likely to reduce MPB biomass. Furthermore, these effects would be sufficient to affect the net metabolic balance of the coastal ecosystem, with important implications for system ecology and sustainable exploitation.
    • Impact of external sources of infection on the dynamics of bovine tuberculosis in modelled badger populations

      Hardstaff, Joanne L.; Bulling, Mark T.; Marion, Glenn; Hutchings, Michael R.; White, Piran C. L. (2013-05-23)
      Background The persistence of bovine TB (bTB) in various countries throughout the world is enhanced by the existence of wildlife hosts for the infection. In Britain and Ireland, the principal wildlife host for bTB is the badger (Meles meles). The objective of our study was to examine the dynamics of bTB in badgers in relation to both badger-derived infection from within the population and externally-derived, trickle-type, infection, such as could occur from other species or environmental sources, using a spatial stochastic simulation model. Results The presence of external sources of infection can increase mean prevalence and reduce the threshold group size for disease persistence. Above the threshold equilibrium group size of 6–8 individuals predicted by the model for bTB persistence in badgers based on internal infection alone, external sources of infection have relatively little impact on the persistence or level of disease. However, within a critical range of group sizes just below this threshold level, external infection becomes much more important in determining disease dynamics. Within this critical range, external infection increases the ratio of intra- to inter-group infections due to the greater probability of external infections entering fully-susceptible groups. The effect is to enable bTB persistence and increase bTB prevalence in badger populations which would not be able to maintain bTB based on internal infection alone. Conclusions External sources of bTB infection can contribute to the persistence of bTB in badger populations. In high-density badger populations, internal badger-derived infections occur at a sufficient rate that the additional effect of external sources in exacerbating disease is minimal. However, in lower-density populations, external sources of infection are much more important in enhancing bTB prevalence and persistence. In such circumstances, it is particularly important that control strategies to reduce bTB in badgers include efforts to minimise such external sources of infection.
    • The impact of freshwater mussels (order Unionoida) on river bed characteristics and sediment flux: A flume-based study.

      Leng, Andrea; Davies-Vollum, K. Siân; Ramsey, Andrew; University of Derby (2018-05-05)
      Unionoid mussels are considered keystone species due to their ability to modify and link pelagic, benthic and hyporheic environments in freshwater systems, [1,2,3] yet empirical data to determine their influence on river bed dynamics and sediment flux is lacking. A recirculating flume-based study using fifty individuals of the unionoid species Anodonta anatina investigated the impact of this species on bedform development and particle flux of a polymodal substrate representative of the grain size distribution of the mussel's river habitat. River seston was added to the flume at weekly intervals, and water and substrate conditions were monitored for the eight-week duration of the study. The control experiment had mussels absent from the flume. It was found that the presence of A. anatina increased the organic content of the substrate through deposition of pseudofaeces, and led to significant reductions in near-bed velocity, boundary shear-stress and the amount of suspended and dissolved solids in the water column. However, despite these impacts a greater quantity of sediment and a larger range of grainsizes entered the flume's sediment trap compared to the control experiment when mussels were absent. The impact of mussel bioturbation appears to outweigh any sediment stabilisation effects arising from the increased organic content of the substrate and the reduced near bed velocities. Additionally, sediment grainsize and longitudinal wetted profile measurements indicate that the mussels increased bed roughness and heterogeneity of the substrate. Given that freshwater mussels can exist at very high densities within rivers, [3] increased mixing and mobilisation of bedload, improved habitat heterogeneity and the transferral of material from the water to the substrate by mussels implies they constitute a critical element in the sediment and nutrient dynamics of fluvial systems. References: 1. Vaughn, C.C., Nichols, S.J. & Spooner, D.E., 2008. Community and foodweb ecology of freshwater mussels. Journal of the North American Benthological Society, 27(2), pp.409-423. 2. Gutierrez, J.L. et al., 2003. Mollusks as ecosystem engineers: the role of shell production in aquatic habitats. Oikos, 101(1), pp.79-90. 3. Aldridge, D.C. et al, 2007. Freshwater mussel abundance predicts biodiversity in UK lowland rivers. Aquatic Conservation-Marine and Freshwater Ecosystems, 17(January), pp.554-564.
    • The impacts of commercial woodland management on butterfly biodiversity.

      Taylor, Donna L.; Ramsey, Andrew; Convery, Ian; Lawrence, Anna; Weatheral, Andrew; University of Cumbria; Forestry Research (2013)
      Although the effects on biodiversity in woodland managed for conservation have been studied for a range of species, there is very little empirical data on the potential impacts of commercial woodland management on biodiversity in the UK. This study measured species richness and abundance of diurnal butterflies as a proxy for the habitat quality of three different woodland management techniques in the Morecambe Bay limestone woodland region. Butterflies were sampled at two sites; Gait Barrows and Witherslack, where three woodland management techniques were carried out: low management woodland (woodland with no recent intervention); traditional coppice management for conservation; and commercial woodland management. Both coppice management for conservation and commercial management had significantly higher butterfly species richness and abundance when compared to low management woodland; neither butterfly species richness nor abundance were significantly different between the traditional coppice management for conservation and commercial woodland management. UK Biodiversity Action Plan fritillary species (high brown fritillary Argynnis adippe; pearl bordered fritillary Boloria euphrosyne; and small pearl bordered fritillary Boloria selene) were not significantly different between the traditional coppice management for conservation and commercial management.
    • Impacts of lagoon opening and implications for coastal management: case study from Muni-Pomadze lagoon, Ghana

      Davies-Vollum, K. Siân; Zhang, Zihao; Agyekumhene, Andrews; University of Derby; University of Virginia; Wildlife Division (Forestry Commission)Winneba,Ghana (Springer, 2018-09-18)
      Lagoon-barrier systems are a dynamic coastal environment. When an ephemeral connection between a lagoon and the ocean develops, it has significant impact on hydrology, sedimentology and ecology. Increasingly, human actions and sea level rise also influence lagoons with the potential to increase their connectivity with the ocean. TheMuni-Pomadze lagoon in central Ghana is a small lagoon-barrier system that is intermittently open to the ocean. Following opening in 2014 the lagoon was open to the ocean for more than two years. Causes for the unusually long period of lagoon opening are unclear although human intrevention has played a role. Field observation, digital mapping and GIS analysis of the shoreline during the two year period of lagoon opening has enabled an understanding of how the lagoon-ocean connection has impacted coastal morphology, erosion and sedimentation. Opening has resulted in rapid changes to the location of the barrier breaching (tidal inlet), erosion on the barrier and sedimentation in the lagoon. Such modifications have implications for local resources and ecosystem services that underpin the livelihood and wellbeing of local communities. Elucidating how a connection to the ocean impacts lagoons and the coastal communities they support are important to managing lagoons not only in Ghana but across West Africa.
    • The implementation of decentralised biogas plants in Assam, NE India: The impact and effectiveness of the National Biogas and Manure Management Programme

      Raha, Debadayita; Mahanta, Pinakeswar; Clarke, Michele L; University of Nottingham (Elsevier, 2014-02-06)
      The Indian Government's National Biogas and Manure Management Programme (NBMMP) seeks to deliver renewable energy services to households across the country by facilitating the deployment of family-sized (<6m3) anaerobic (biogas) digesters. NBMMP policy is implemented at three levels, from government and state nodal agency, via private contractors to households, creating multiple institutional arrangements. We analysed the scheme in Assam, north-east India, focusing on how policy was implemented across two districts and interviewing stakeholders in rural households, state and non-state institutions. The top-down, supply-side approach to policy enables government to set targets and require individual states to deploy the scheme, which benefits households who can afford to participate. NBMMP delivered improved energy service outcomes to a majority of households, although the level of knowledge and understanding of the technology amongst users was limited. Training and education of householders, and particularly women, is needed in relation to the maintenance of digesters, feedstock suitability and the environmental and potential livelihood benefits of digestate. A revised bottom-up approach to policy, which highlights the contextual and demand-side issues around adopting the technology, may deliver monetary benefits from market competition and enable development of community-focused microfinance schemes to improve the affordability of biogas systems.
    • Implications of traditional commercial practices on the current environmental status of River Yamuna in the Delhi-Mathura-Agra region, India

      Mehra, Aradhana; Banerjee, Deepak; University of Derby (International Water Association, 2014-03)
      The River Yamuna is regarded as a holy river in Indian mythology. It originates in the Himalayas and several important cities, pilgrimage centres and temple towns are located along its banks. It is a source of water supply to these cities and also receives their wastewaters from domestic and industrial activities. This study aims to assess the environmental and human health implications of traditional commercial practices such as electroplating and jewellery making in the cottage industries along the banks of River Yamuna in the Delhi-Mathura-Agra region. Human exposure to contaminants from overbank soil and also through the food chain from crops grown on floodplains are considered through analyses of overbank and floodplain soils with special reference to toxic trace metals such as silver, cadmium, copper, and zinc. The findings of study show that the overbank and floodplain soils at the temple town of Mathura are highly contaminated with silver and cadmium, and are above normal background concentrations for copper and zinc. This leads to suggest that the traditional and cultural activities of jewellery-making and electroplating works at Mathura are contributing a high metal load to its overbank and floodplain soils and are a cause for concern for human health.
    • The importance of Forest School and the pathways to nature connection

      Cudworth, Dave; Lumber, Ryan; DeMontfort University; University of Derby (Springer Science and Business Media LLC, 2021-02-18)
      Over the past 25 years Forest School in the UK has been growing in popularity as part of a wider resurgence of interest in outdoor learning. A key driver behind this recurrence of interest has been a growing concern over the lack of child exposure to outdoor experiences and with the natural world and their ensuing nature-deficit disorder. This article considers Forest School as linked with the concept of nature connection that is the sensation of belonging to a wider natural community. This sense of belonging developed by being in nature can also be a key factor in promoting attachment and sense of place which in turn is associated with the promotion of health, wellbeing and pro-environmental behaviours. As such the origins towards achieving nature connection are a formal part of the Forest School Association’s (FSA 2016). Forest School principals, with growing research linking Forest School and nature connection as concomitant. Recent work has suggested that contact, emotion, meaning, compassion, and beauty are key pathways for the formation of nature connection and there is a strong need to better understand children’s nature connection in this context. Further, from the premise that what goes on in spaces and places is fundamentally linked to both social and spatial processes, this article also attempts to understand the spatialities of Forest School in order to frame the development of nature connection within a socio-spatial analytic.
    • Improving the reliability of eDNA data interpretation

      Burian, Alfred; Mauvisseau, Quentin; Bulling, Mark; Domisch, Sami; Qian, Song; Sweet, Michael; University of Derby; Marine Ecology Department, Lurio University, Nampula, Mozambique; Helmholtz Centre for Environmental Research, Leipzig, Germany; Natural History Museum, University of Oslo, Oslo, Norway; et al. (Wiley, 2021-03-25)
      Global declines in biodiversity highlight the need to effectively monitor the density and distribution of threatened species. In recent years, molecular survey methods detecting DNA released by target‐species into their environment (eDNA) have been rapidly on the rise. Despite providing new, cost‐effective tools for conservation, eDNA‐based methods are prone to errors. Best field and laboratory practices can mitigate some, but the risks of errors cannot be eliminated and need to be accounted for. Here, we synthesize recent advances in data processing tools that increase the reliability of interpretations drawn from eDNA data. We review advances in occupancy models to consider spatial data‐structures and simultaneously assess rates of false positive and negative results. Further, we introduce process‐based models and the integration of metabarcoding data as complementing approaches to increase the reliability of target‐species assessments. These tools will be most effective when capitalizing on multi‐source data sets collating eDNA with classical survey and citizen‐science approaches, paving the way for more robust decision‐making processes in conservation planning.
    • In situ observations of coral bleaching in the central Saudi Arabian Red Sea during the 2015/2016 global coral bleaching event.

      Monroe, Alison A.; Ziegler, Maren; Roik, Anna; Röthig, Till; Hardenstine, Royale S.; Emms, Madeleine A.; Jensen, Thor; Voolstra, Christian R.; Berumen, Michael L.; King Abdullah University of Science and Technology (KAUST); et al. (PLOS ONE, 2018-04-19)
      Coral bleaching continues to be one of the most devastating and immediate impacts of climate change on coral reef ecosystems worldwide. In 2015, a major bleaching event was declared as the “3rd global coral bleaching event” by the United States National Oceanic and Atmospheric Administration, impacting a large number of reefs in every major ocean. The Red Sea was no exception, and we present herein in situ observations of the status of coral reefs in the central Saudi Arabian Red Sea from September 2015, following extended periods of high temperatures reaching upwards of 32.5°C in our study area. We examined eleven reefs using line-intercept transects at three different depths, including all reefs that were surveyed during a previous bleaching event in 2010. Bleaching was most prevalent on inshore reefs (55.6% ± 14.6% of live coral cover exhibited bleaching) and on shallower transects (41% ± 10.2% of live corals surveyed at 5m depth) within reefs. Similar taxonomic groups (e.g., Agariciidae) were affected in 2015 and in 2010. Most interestingly, Acropora and Porites had similar bleaching rates (~30% each) and similar relative coral cover (~7% each) across all reefs in 2015. Coral genera with the highest levels of bleaching (>60%) were also among the rarest (<1% of coral cover) in 2015. While this bodes well for the relative retention of coral cover, it may ultimately lead to decreased species richness, often considered an important component of a healthy coral reef. The resultant long-term changes in these coral reef communities remain to be seen.
    • Increased copulation duration before ejaculate transfer is associated with larger spermatophores, and male genital titillators, across bushcricket taxa

      Vahed, Karim; Lehmann, Gerlind; Gilbert, James D. J.; Lehmann, A. W.; University of Derby (Wiley Blackwell, 2011-09)
      Copulation duration varies considerably across species, but few comparative studies have examined factors that might underlie such variation. We examined the relationship between copulation duration (prior to spermatophore transfer), the complexity of titillators (sclerotized male genital contact structures), spermatophore mass and male body mass across 54 species of bushcricket. Using phylogenetic comparative analyses, we found that copulation duration was much longer in species with titillators than those without, but it was not longer in species with complex compared with simple titillators. A positive relationship was found between spermatophore size and copulation duration prior to ejaculate transfer, which supports the hypothesis that this represents a period of mate assessment. The slope of this relationship was steeper in species with simple rather than complex titillators. Although the data suggest that the presence of titillators is necessary to maintain long copulation prior to ejaculate transfer, mechanisms underlying this association remain unclear.
    • Increases in egg production in multiply mated female bushcrickets Leptophyes punctatissima are not due to substances in the nuptial gift

      Vahed, Karim; University of Derby (Wiley, 2003-02)
      1. A positive effect of the degree of polyandry on egg production is widespread in insects, particularly in species in which the male provides a nuptial gift. 2. This study aimed to determine whether or not this effect is due to females using nutrients from the nuptial gift (spermatophore and spermatophylax) to manufacture more eggs in the bushcricket Leptophyes punctatissima. 3. Females were permitted either a single or a double mating (with two different males) and, in both mating categories, were either prevented from consuming any part of the spermatophore or were permitted to consume the entire spermatophore. 4. Doubly mated females were found to lay over twice as many eggs over a 4-week period compared with singly mated females. This difference did not appear to be caused by the consumption of extra nuptial gift material: mating was found to have a significant positive effect on the number of eggs laid, while nuptial gift feeding had no effect.
    • Indirect effects of non-lethal predation on bivalve activity and sediment reworking

      Maire, O.; Merchant, J. N.; Bulling, Mark T.; Teal, L. R.; Grémare, A.; Duchêne, J. C.; Solan, Martin (2013-05-24)
      Deposit-feeders are the dominant bioturbators of aquatic sediments, where they profoundly impact biogeochemical processes, but they are also vulnerable to both lethal and non-lethal predation by a large variety of predators. In this study, we performed a series of experiments to test the effects of predation avoidance on the feeding activity and sediment reworking intensity of the deposit-feeding bivalve Macoma balthica. Feeding activity at the sediment–water interface and sediment reworking intensity (vertical displacements of inert particle tracers) were monitored using image analysis techniques for treatments including and excluding the predatory shrimp, Crangon crangon. Detection of C. crangon by M. balthica resulted in an immediate retraction of the feeding siphon and a reduction in feeding activity. M. balthica also buried deeper into the sediment in the presence of C. crangon. This predator avoidance behaviour indirectly affected sediment reworking modes and rates, increasing the thickness of the bioturbated sediment layer as well as the non-local transport of sediment particles at depth. Conversely, feeding activity and sediment reworking processes remained unaffected when C. crangon was present, but isolated from the sediment, suggesting that predator perception in M. balthica is tactile (i.e. induced by direct encounter) rather than being chemosensory. Collectively, these results demonstrate that predatory avoidance behaviour by benthic infauna can significantly impact benthic bioturbation and the incorporation of organic matter into the benthic food web.
    • Inducing broadcast coral spawning ex situ: Closed system mesocosm design and husbandry protocol.

      Craggs, Jamie; Guest, James R.; Davis, Michelle; Simmons, Jeremy; Dashti, Ehsan; Sweet, Michael J.; University of Derby; Horniman Museum and Gardens; Newcastle University; SECORE International; et al. (Wiley, 2017-11-15)
      For many corals, the timing of broadcast spawning correlates strongly with a number of environmental signals (seasonal temperature, lunar, and diel cycles). Robust experimental studies examining the role of these putative cues in triggering spawning have been lacking until recently because it has not been possible to predictably induce spawning in fully closed artificial mesocosms. Here, we present a closed system mesocosm aquarium design that utilizes microprocessor technology to accurately replicate environmental conditions, including photoperiod, seasonal insolation, lunar cycles, and seasonal temperature from Singapore and the Great Barrier Reef (GBR), Australia. Coupled with appropriate coral husbandry, these mesocosms were successful in inducing, for the first time, broadcast coral spawning in a fully closed artificial ex situ environment. Four Acropora species (A. hyacinthus, A. tenuis, A. millepora, and A. microclados) from two geographical locations, kept for over 1 year, completed full gametogenic cycles ex situ. The percentage of colonies developing oocytes varied from ~29% for A. hyacinthus to 100% for A. millepora and A. microclados. Within the Singapore mesocosm, A. hyacinthus exhibited the closest synchronization to wild spawning, with all four gravid colonies releasing gametes in the same lunar month as wild predicted dates. Spawning within the GBR mesocosm commenced at the predicted wild spawn date but extended over a period of 3 months. Gamete release in relation to the time postsunset for A. hyacinthus, A. millepora, and A. tenuis was consistent with time windows previously described in the wild. Spawn date in relation to full moon, however, was delayed in all species, possibly as a result of external light pollution. The system described here could broaden the number of institutions on a global scale, that can access material for broadcast coral spawning research, providing opportunities for institutions distant from coral reefs to produce large numbers of coral larvae and juveniles for research purposes and reef restoration efforts.
    • Influence of accuracy, repeatability and detection probability in the reliability of species-specific eDNA based approaches

      Mauvisseau, Quentin; Burian, Alfred; Gibson, Ceri; Brys, Rein; Ramsey, Andrew; Sweet, Michael; University of Derby; Freshwater Biological Association, Cumbria; Research Institute for Nature and Forest, Belgium (Springer, 2019-01-24)
      Environmental DNA (eDNA) barcoding has a high potential to increase the cost-efficiency of species detection and monitoring in aquatic habitats. However, despite vast developments in the field, many published assays often lack detailed validation and there is little to no commonly (agreed upon) standardization of protocols. In this study, we evaluated the reliability of eDNA detection and quantification using published primers and assays targeting the Freshwater Pearl Mussel as a model organism. We first assessed limits of detection for two different target genes (COI and 16S) following the MIQE guidelines, and then tested the reliability of quantification in a double-blind mesocosm experiment. Our results reveal that different methodological indicators, namely accuracy, repeatability and detection probability affected the reliability of eDNA measurement at the different levels tested. The selection of the optimal analytical method was mainly determined by detection probability. Both the COI and 16S assays were highly specific for the targeted organism and showed similar accuracy and repeatability, whilst the limit of detection was clearly lower for the COI based approach. In contrast, the reliability of eDNA quantification hinged on repeatability, reflected by the scattering (r2 = 0.87) around the relationship between eDNA and mussel density in mesocosms. A bootstrapping approach, which allowed for the assignment of measures associated with repeatability of samples, revealed that variability between natural replicates (i.e. accuracy) strongly influenced the number of replicates required for a reliable species detection and quantification in the field.
    • Influence of macrofaunal assemblages and environmental heterogeneity on microphytobenthic production in experimental systems

      Dyson, Kirstie E.; Bulling, Mark T.; Solan, Martin; Hernandez-Milian, Gema; Raffaelli, D.; White, Piran C. L.; Paterson, David M. (2013-05-24)
      Despite the complexity of natural systems, heterogeneity caused by the fragmentation of habitats has seldom been considered when investigating ecosystem processes. Empirical approaches that have included the influence of heterogeneity tend to be biased towards terrestrial habitats; yet marine systems offer opportunities by virtue of their relative ease of manipulation, rapid response times and the well-understood effects of macrofauna on sediment processes. Here, the influence of heterogeneity on microphytobenthic production in synthetic estuarine assemblages is examined. Heterogeneity was created by enriching patches of sediment with detrital algae (Enteromorpha intestinalis) to provide a source of allochthonous organic matter. A gradient of species density for four numerically dominant intertidal macrofauna (Hediste diversicolor, Hydrobia ulvae, Corophium volutator, Macoma balthica) was constructed, and microphyto- benthic biomass at the sediment surface was measured. Statistical analysis using generalized least squares regression indicated that heterogeneity within our system was a significant driving factor that interacted with macrofaunal density and species identity. Microphytobenthic biomass was highest in enriched patches, suggesting that nutrients were obtained locally from the sediment–water interface and not from the water column. Our findings demonstrate that organic enrichment can cause the development of heterogeneity which influences infaunal bioturbation and consequent nutrient generation, a driver of microphytobenthic production.