• 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.
    • Tracing the origin of olive ridley turtles entangled in ghost nets in the Maldives: A phylogeographic assessment of populations at risk

      Stelfox, Martin; Burian, Alfred; Shanker, Kartik; Rees, Alan F.; Jean, Claire; Willson, Maïa S.; Manik, Nashwa Ahmed; Sweet, Michael; University of Derby; Olive Ridley Project, 11 Dane Close, Bramhall, Stockport, Cheshire; et al. (Elsevier BV, 2020-04-07)
      Abandoned, lost or discarded fishing nets, (ghost nets) represent a major threat to marine vertebrates. However, thorough assessments of their impact on threatened species are largely missing. In the Maldives, olive ridley sea turtles (Lepidochelys olivacea) are frequently caught in ghost nets however the archipelago does not support a significant nesting population. Our aim in this study was to determine the origin of olive ridleys entangled in ghost nets found in the Maldives and evaluate potential impacts on respective source populations. Based on a citizen science and conservation program, we recorded 132 olive ridley turtles entangled in ghost nets in just one year. Genetic analyses (mtDNA) of entangled individuals and of potential source populations revealed that most captured olive ridleys originated from Sri Lanka and eastern India. Oman could be excluded as source population, even during the prevalence of the south west monsoon. Based on our results and already available published literature, we were able to estimate that the recorded ghost net entanglements accounted for a relatively small amount (0.48%) of the eastern Indian population. However, the entangled turtles accounted for a much larger percentage (41%) of the Sri Lankan populations. However, it should be noted that our estimates of population-level mortality are linked to substantial uncertainty due to the lack of reliable information on population dynamics. Consequently, any precautionary protection measures applied should be complemented with improved quantification of turtle recruitment and life-stage specific mortalities.
    • Reliable eDNA detection and quantification of the European weather loach (Misgurnus fossilis)

      Brys, Rein; Halfmaerten, David; Neyrinck, Sabrina; Mauvisseau, Quentin; Auwerx, Johan; Sweet, Michael; Mergeay, Joachim; Research Institute for Nature and Forest, Geraardsbergen, Belgium; University of Derby; SureScreen Scientifics Ltd (Wiley, 2020-03-10)
      The European weather loach (Misgurnus fossilis) is a cryptic and poorly known fish species of high conservation concern. The species is experiencing dramatic population collapses across its native range to the point of regional extinction. Although environmental DNA (eDNA)‐based approaches offer clear advantages over conventional field methods for monitoring rare and endangered species, accurate detection and quantification remain difficult and quality assessment is often poorly incorporated. In this study, we developed and validated a novel digital droplet PCR (ddPCR) eDNA‐based method for reliable detection and quantification, which allows accurate monitoring of M. fossilis across a number of habitat types. A dilution experiment under laboratory conditions allowed the definition of the limit of detection (LOD) and the limit of quantification (LOQ), which were set at concentrations of 0.07 and 0.14 copies μl–1, respectively. A series of aquarium experiments revealed a significant and positive relationship between the number of individuals and the eDNA concentration measured. During a 3 year survey (2017–2019), we assessed 96 locations for the presence of M. fossilis in Flanders (Belgium). eDNA analyses on these samples highlighted 45% positive detections of the species. On the basis of the eDNA concentration per litre of water, only 12 sites appeared to harbour relatively dense populations. The other 31 sites gave a relatively weak positive signal that was typically situated below the LOQ. Combining sample‐specific estimates of effective DNA quantity (Qe) and conventional field sampling, we concluded that each of these weak positive sites still likely harboured the species and therefore they do not represent false positives. Further, only seven of the classified negative samples warrant additional sampling as our analyses identified a substantial risk of false‐negative detections (i.e., type II errors) at these locations. Finally, we illustrated that ddPCR outcompetes conventional qPCR analyses, especially when target DNA concentrations are critically low, which could be attributed to a reduced sensitivity of ddPCR to inhibition effects, higher sample concentrations being accommodated and higher sensitivity obtained.
    • Heat waves are a major threat to turbid coral reefs in Brazil

      Duarte, Gustavo A. S.; Villela, Helena D. M.; Deocleciano, Matheus; Silva, Denise; Barno, Adam; Cardoso, Pedro M.; Vilela, Caren L. S.; Rosado, Phillipe; Messias, Camila S. M. A.; Chacon, Maria Alejandra; et al. (Frontiers Media SA, 2020-03-30)
      Coral reefs are threatened by climate change on a global scale with thermal stress events and mass coral bleaching being widely reported. The reefs off the east coast of Brazil (and other turbid areas) have, however, historically escaped such thermal stress events, with relatively low levels of background coral mortality (5–10%). This has recently changed. Here we show that, in 2019, degree heating weeks (DHW) of 19.65 coincided with catastrophic declines in coral cover, especially in the major reef building hydrocoral Millepora alcicornis. The decline was due to bleaching associated with exposure to high temperature stress culminating in DHW values exceeding 15 for a period of 50 days. At two independent sites, surveys showed upwards of 83.5 ± 9.0 and 89.1 ± 3.9% mortality, and a third site showed relatively lower (albeit still high) mortality rates of 43.3 ± 12.0%. The mass die-off in 2019 is unprecedented in the South Atlantic reefs and coincides with increased heating events.
    • Estimating food production in an urban landscape

      Grafius, Darren R.; Edmondson, Jill L.; Norton, Briony A.; Clark, Rachel; Mears, Meghann; Leake, Jonathan R.; Corstanje, Ron; Harris, Jim A.; Warren, Philip H.; University of Sheffield; et al. (Springer Science and Business Media LLC, 2020-03-20)
      There is increasing interest in urban food production for reasons of food security, environmental sustainability, social and health benefits. In developed nations urban food growing is largely informal and localised, in gardens, allotments and public spaces, but we know little about the magnitude of this production. Here we couple own-grown crop yield data with garden and allotment areal surveys and urban fruit tree occurrence to provide one of the first estimates for current and potential food production in a UK urban setting. Current production is estimated to be sufficient to supply the urban population with fruit and vegetables for about 30 days per year, while the most optimistic model results suggest that existing land cultivated for food could supply over half of the annual demand. Our findings provide a baseline for current production whilst highlighting the potential for change under the scaling up of cultivation on existing land.
    • The evolution of pair-living, sexual monogamy, and cooperative infant care: Insights from research on wild owl monkeys, titis, sakis, and tamarins

      Fernandez-Duque, Eduardo; Huck, Maren; Van Belle, Sarie; Di Fiore, Anthony; University of Derby; Yale University; University of Austin, Texas (Wiley, 2020-03-19)
      “Monogamy” and pair bonding have long been of interest to anthropologists and primatologists. Their study contributes to our knowledge of human evolutionary biology and social evolution without the cultural trappings associated with studying human societies directly. Here, we first provide an overview of theoretical considerations, followed by an evaluation of recent comparative studies of the evolution of “social monogamy”; we are left with serious doubts about the conclusions of these studies that stem from the often poor quality of the data used and an overreliance on secondary sources without vetting the data therein. We then describe our field research program on four “monogamous” platyrrhines (owl monkeys, titis, sakis, and tamarins), evaluate how well our data support various hypotheses proposed to explain “monogamy,” and compare our data to those reported on the same genera in comparative studies. Overall, we found a distressing lack of agreement between the data used in comparative studies and data from the literature for the taxa that we work with. In the final section, we propose areas of research that deserve more attention. We stress the need for more high‐quality natural history data, and we urge researchers to be cautious about the uncritical use of variables of uncertain internal validity. Overall, it is imperative that biological anthropologists establish and follow clear criteria for comparing and combining results from published studies and that researchers, reviewers, and editors alike comply with these standards to improve the transparency, reproducibility, and interpretability of causal inferences made in comparative studies.
    • Rain-fed granite rock basins accumulate a high diversity of dormant microbial eukaryotes

      Velasco-González, Ismael; Sanchez-Jimenez, Abel; Singer, David; Murciano, Antonio; Díez-Hermano, Sergio; Lara, Enrique; Martín-Cereceda, Mercedes; Departamento de Genética, Fisiología y Microbiología. Facultad de Ciencias Biológicas, Universidad Complutense de Madrid (UCM), C/ José Antonio Novais 12, 28040, Madrid, Spain; Departamento de Biodiversidad, Ecología y Evolución. Facultad de Ciencias Biológicas, UCM, Madrid, Spain; University of Neuchâtel, Rue Emile-Argand 11, CH-2000, Neuchâtel, Switzerland; et al. (Springer Science and Business Media LLC, 2019-12-03)
      Rain fed granite rock basins are ancient geological landforms of worldwide distribution and structural simplicity. They support habitats that can switch quickly from terrestrial to aquatic along the year. Diversity of animals and plants, and the connexion between communities in different basins have been widely explored in these habitats, but hardly any research has been carried out on microorganisms. The aim of this study is to provide the first insights on the diversity of eukaryotic microbial communities from these environments. Due to the ephemeral nature of these aquatic environments, we predict that the granitic basins should host a high proportion of dormant microeukaryotes. Based on an environmental DNA diversity survey, we reveal diverse communities with representatives of all major eukaryotic taxonomic supergroups, mainly composed of a diverse pool of low abundance OTUs. Basin communities were very distinctive, with alpha and beta diversity patterns non-related to basin size or spatial distance respectively. Dissimilarity between basins was mainly characterised by turnover of OTUs. The strong microbial eukaryotic heterogeneity observed among the basins may be explained by a complex combination of deterministic factors (diverging environment in the basins), spatial constraints, and randomness including founder effects. Most interestingly, communities contain organisms that cannot coexist at the same time because of incompatible metabolic requirements, thus suggesting the existence of a pool of dormant organisms whose activity varies along with the changing environment. These organisms accumulate in the pools, which turns granitic rock into high biodiversity microbial islands whose conservation and study deserve further attention.
    • Sexual dimorphism in the loud calls of Azara’s owl monkeys (Aotus azarae): evidence of sexual selection?

      Garcia de la Chica, Alba; Huck, Maren; Depeine, Catherine; Rotundo, Marcelo; Adret, Patrice; Fernandez-Duque, Eduardo; University of Derby (Springer Science and Business Media LLC, 2019-11-15)
      Primates use different types of vocalizations in a variety of contexts. Some of the most studied types have been the long distance or loud calls. These vocalizations have been associated with mate defense, mate attraction, and resource defense, and it is plausible that sexual selection has played an important role in their evolution. Focusing on identified individuals of known sex and age, we evaluated the sexual dimorphism in a type of loud calls (hoots) in a population of wild owl monkeys (Aotus azarae) in Argentina. We found evidence of sexual dimorphism in call structure, with females and males only emitting one type of call, each differing in dominant frequency and Shannon entropy. In addition, both age-related and sex-specific differences in call usage were also apparent in response to the removal of one group member. Future acoustic data will allow us to assess if there are individual characteristics and if the structure of hoot calls presents differences in relation to the social condition of owl monkeys or specific sex responses to variants of hoot calls’ traits. This will provide deeper insights into the evolution of vocal mechanisms regulating pair bonding and mate choice strategies in this and other primate species.
    • Minimum drift times infer trajectories of ghost nets found in the Maldives

      Stelfox, Martin; Lett, Christophe; Reid, Geraldine; Souch, Graham; Sweet, Michael; University of Derby; Olive Ridley Project, Bramhall, Stockport, Cheshire; MARBEC, IRD, Ifremer, Univ Montpellier, CNRS, Sète, France; National Museums Liverpool (Elsevier BV, 2020-03-07)
      This study explores methods to estimate minimum drift times of ghost nets found in the Maldives with the aim of identifying a putative origin. We highlight that percentage cover of biofouling organisms and capitulum length of Lepas anatifera are two methods that provide these estimates. Eight ghost nets were collected in the Maldives and estimated drift times ranged between 7.5 and 101 days. Additionally, Lagrangian simulations identified drift trajectories of 326 historical ghost nets records. Purse seine fisheries (associated with Korea, Mauritius, the Philippines, Spain, France and Seychelles) and gill nets from Sri Lanka were identified as 'high risk' fisheries with regard to likley origins of ghost nets drifting into the Maldives. These fisheries are active in areas where dense particle clusters occured (drift trajectories between 30 and 120 days). Interestingly, ghost nets drifting less than 30 days however, remained inside the exclusive economic zone of the Maldivian archipelago highlighting potential illegal, unreported and unregulated fishing activity is occuring in this area. This study therefore points to the urgent need for gear loss reporting to be undertaken, especially by purse seine and gill net fisheries in order to ascertain the source of this major threat to marine life. This should also be coupled with an improvment in the data focused on spatial distribution of the abandoned, lost or discarded fishing gear originating from both large- and small-scale fisheries.
    • Complexity of river ciliate communities at a National Park highlights the need for microbial conservation

      Quintela-Alonso, P.; Perez-Uz, B.; Sanchez-Jimenez, A.; Murciano, A.; Centeno, JD.; Garcia-Rodriguez, M.; Montero, E.; Munoz, B.; Olmedo, C.; Refoyo, P.; et al. (Wiley, 2017-12-07)
      Microorganisms play pivotal roles in aquatic ecosystems. Free‐living protists are the main components of the eukaryotic microbial communities at the base of freshwater ecosystems. Ciliate grazing channels a large proportion of organic matter into multicellular organisms. Surprisingly, ciliates and other microorganisms are neglected in global conservation schemes. Interstitial ciliates were sampled in three sites of varying human pressure on the River Manzanares (La Pedriza National Park, Spain). Abundances of trophic groups and species were adjusted to a generalized linear model (GLM Poisson regression). Ciliate communities were rich in species (74 morphotypes) and although traditional microscopy retrieved a high number of species that appeared only once or in low numbers, rarefaction analyses estimated much larger species richness. These results illustrate that rarefaction assays are a useful first step for exploring the extent of the ciliate cryptic diversity in freshwater ecosystems. Benthic ciliate communities changed significantly, both spatially and at a short temporal scale. The fluctuating nature of the community was manifested by the presence of many ephemeral species at the same river site, revealing a complex and transient community structure. No significant short‐term changes were observed in the physical–chemical properties. Therefore, even slight differences in the abiotic variables may cause rapid shifts of ciliate species. Overall, human pressure had an effect on the interstitial (or benthic) ciliates that resulted in a reduction of species richness and their abundance.
    • Major evolutionary transitions of life, metabolic scaling and the number and size of mitochondria and chloroplasts.

      Okie, J.; Smith, V.; Martin-Cereceda, M; University of Kansas, USA; University of Madrid, Spain; Arizona State University, Tempe, AZ, USA (The Royal Society Publishing, 2016-05-25)
      We investigate the effects of trophic lifestyle and two types of major evolutionary transitions in individuality—the endosymbiotic acquisition of organelles and development of multicellularity—on organellar and cellular metabolism and allometry. We develop a quantitative framework linking the size and metabolic scaling of eukaryotic cells to the abundance, size and metabolic scaling of mitochondria and chloroplasts and analyse a newly compiled, unprecedented database representing unicellular and multicellular cells covering diverse phyla and tissues. Irrespective of cellularity, numbers and total volumes of mitochondria scale linearly with cell volume, whereas chloroplasts scale sublinearly and sizes of both organelles remain largely invariant with cell size. Our framework allows us to estimate the metabolic scaling exponents of organelles and cells. Photoautotrophic cells and organelles exhibit photosynthetic scaling exponents always less than one, whereas chemoheterotrophic cells and organelles have steeper respiratory scaling exponents close to one. Multicellularity has no discernible effect on the metabolic scaling of organelles and cells. In contrast, trophic lifestyle has a profound and uniform effect, and our results suggest that endosymbiosis fundamentally altered the metabolic scaling of free-living bacterial ancestors of mitochondria and chloroplasts, from steep ancestral scaling to a shallower scaling in their endosymbiotic descendants.
    • The Bacillus subtilis DnaD and DnaB Proteins Exhibit Different DNA Remodelling Activities

      Carneiro, Maria J.V.M.; Turner, Ian J.; Allen, Stephanie; Roberts, Clive J.; Soultanas, Panos; University of Nottingham (Elsevier, 2005-08-05)
      Primosomal protein cascades load the replicative helicase onto DNA. In Bacillus subtilis a putative primosomal cascade involving the DnaD-DnaB-DnaI proteins has been suggested to participate in both the DnaA and PriA-dependent loading of the replicative helicase DnaC onto the DNA. Recently we discovered that DnaD has a global remodelling DNA activity suggesting a more widespread role in bacterial nucleoid architecture. Here, we show that DnaB forms a “square-like” tetramer with a hole in the centre and suggest a model for its interaction with DNA. It has a global DNA remodelling activity that is different from that of DnaD. Whereas DnaD opens up supercoiled DNA, DnaB acts as a lateral compaction protein. The two competing activities can act together on a supercoiled plasmid forming two topologically distinct poles; one compacted with DnaB and the other open with DnaD. We propose that the primary roles of DnaB and DnaD are in bacterial nucleoid architecture control and modulation, and their effects on the initiation of DNA replication are a secondary role resulting from architectural perturbations of chromosomal DNA.
    • Green roof and ground-level invertebrate communities are similar and are driven by building height and landscape context

      Dromgold, Jacinda R; Threlfall, Caragh G; Norton, Briony, A.; Williams, Nicholas S G; University of Melbourne, Melbourne, Australia; University of Derby (Oxford University Press (OUP), 2020-01-30)
      Green roofs are increasingly promoted for urban biodiversity conservation, but the value of these novel habitats is uncertain. We aimed to test two hypotheses: (i) green roofs can support comparable invertebrate family and order richness, composition and abundances to ground-level habitats and (ii) green roofs planted with native species from local habitats will support a richer invertebrate community at family and order level than other green roofs. We sampled the invertebrate community on green roofs dominated by native grassland or introduced succulent species in Melbourne, Australia, and compared these to the invertebrate community in ground-level sites close by, and sites with similar vegetation types. The only significant differences between the invertebrate communities sampled on green roofs and ground-level habitats were total abundance and fly family richness, which were higher in ground-level habitats. Second hypothesis was not supported as invertebrate communities on green roofs supporting a local vegetation community and those planted with introduced Sedum and other succulents were not detectably different at family level. The per cent cover of green space surrounding each site was consistently important in predicting the richness and abundance of the invertebrate families we focussed on, while roof height, site age and size were influential for some taxa. Our results suggest that invertebrate communities of green roofs in Melbourne are driven largely by their surrounding environment and consequently the effectiveness of green roofs as invertebrate habitat is highly dependent on location and their horizontal and vertical connection to other habitats.
    • Of apples and oranges? The evolution of “monogamy” in non-human primates

      Huck, Maren; Di Fore, Anthony; Fernandez-Duque, Eduardo; University of Derby, Environmental Sustainability Research Centre; University of Texas at Austin; Yale University (Frontiers, 2020-01-10)
      Behavioral ecologists, evolutionary biologists, and anthropologists have been long fascinated by the existence of “monogamy” in the animal kingdom. Multiple studies have explored the factors underlying its evolution and maintenance, sometimes with contradicting and contentious conclusions. These studies have been plagued by a persistent use of fuzzy terminology that often leads to researchers comparing “apples with oranges” (e.g., comparing a grouping pattern or social organization with a sexual or genetic mating system). In this review, we provide an overview of research on “monogamy” in mammals generally and primates in particular, and we discuss a number of problems that complicate comparative attempts to understand this issue. We first highlight why the muddled terminology has hindered our understanding of both a rare social organization and a rare mating system. Then, following a short overview of the main hypotheses explaining the evolution of pair-living and sexualmonogamy, we critically discuss various claims about the principal drivers of “monogamy” that have been made in several recent comparative studies.We stress the importance of using only high quality and comparable data. We then propose that a productive way to frame and dissect the different components of pair-living and sexual or genetic monogamy is by considering the behavioral and evolutionary implications of those components from the perspectives of all participants in a species’ social system. In particular, we highlight the importance of integrating the perspective of “floater” individuals and considering their impacts on local operational sex ratios, competition, and variance in reproductive success across a population. We stress that pair-living need not imply a reduced importance of intrasexual mate competition, a situation that may have implications for the sexual selection potential that have not yet been fully explored. Finally, we note that there is no reason to assume that different taxa and lineages, even within the same radiation, should follow the same pathway to or share a unifying evolutionary explanation for “monogamy”. The study of the evolution of pair-living, sexual monogamy, and genetic monogamy remains a challenging and exciting area of research.
    • Untangling the origin of ghost gear within the Maldivian archipelago and its impact on olive ridley (Lepidochelys olivacea) populations

      Stelfox, M; Bulling, M; Sweet, M; University of Derby; Olive Ridley Project, Cheshire (Inter-Research Science Center, 2019-12-12)
      There is little documentation available on the impact of abandoned, lost or discarded fishing nets (‘ghost nets’) on turtle populations. Here, we utilise data collected over a 5 year period to assess (1) if a particular net type or characteristic was identifiable as entangling more turtles and (2) if particular fishing practices (i.e. types of nets) could be managed to reduce turtle entanglement in the Maldivian archipelago. A total of 131 turtles were entangled in the 752 reported ghost nets, and olive ridley turtles Lepidochelys olivacea appeared to be the most vulnerable (making up 97% of entangled turtles). However, we estimate that the 752 nets in this study, reported over a 51 month period, could have entangled between 3400 and 12200 turtles across the Indian Ocean prior to being detected in the Maldives. Mesh size, seasonality (i.e. north east monsoon), and the presence of floats were all identified as variables significantly affecting the likelihood of turtle entanglement. The probability of entanglement increased as the mesh size increased but decreased when floats were present. Additionally, turtles were more likely to be entangled during the north east monsoon when currents flow from east to west. Cluster analysis indicated that there were at least 11 broadly assigned net types found floating in the study area, and these were dominated by trawl and gill nets. Our analyses highlight the need for a detailed database of existing gear types coupled with gear marking to improve traceability of ghost nets in the Indian Ocean.
    • The development of an eDNA based detection method for the invasive shrimp Dikerogammarus haemobaphes

      Mauvisseau, Quentin; Troth, Chris; Young, Emily; Burian, Alfred; Sweet, Michael; University of Derby; Surescreen Scientifics Ltd, Morley (Regional Euro-Asian Biological Invasions Centre Oy (REABIC), 2019-06-06)
      Dikerogammarus haemobaphes is a freshwater gammarid crustacean native to the Ponto-Caspian region. However, the species is rapidly spreading throughout Western Europe and is classed as a highly invasive species. Here we present a novel eDNA assay aimed at detecting D. haemobaphes and demonstrate its suitability with validation steps conducted in-silico (computer simulations), ex-situ (test of specificity using closely related species) and in-situ (within the field). A survey of freshwater systems in the West-Midlands, United Kingdom, highlighted that D. haemobaphes was present in 26 out of the 39 sites assessed. We conclude that eDNA detection for D. haemobaphes is a promising tool for assessing and mapping the presence/distribution of this invasive amphipod.
    • Early detection of an emerging invasive species: eDNA monitoring of a parthenogenetic crayfish in freshwater systems

      Mauvisseau, Quentin; Sweet, Michael; Lyko, Frank; Andriantsoa, Ranja; Tonges, Sina; University of Derby; Surescreen Scientifics Ltd, Morley; German Cancer Research Center, Germany (Regional Euro-Asian Biological Invasions Centre Oy (REABIC), 2019-06-06)
      Procambarus virginalis, also known as the Marmorkrebs is a highly invasive crayfish species characterized by parthenogenetic reproduction. As conservation management plans rely on the accuracy of the presence and distribution information of invasive species, a reliable method is needed for detecting such species in aquatic systems. We developed and validated a qPCR-based assay for monitoring P. virginalis at low abundance, by detecting their eDNA traces left in freshwater systems. We were able to implement this new assay in-situ at two separate lakes in Germany, where the crayfish were known to be present. Furthermore, we did not detect the pathogenic fungus Aphanomyces astaci in the locations where the Marmorkrebs were detected. We conclude that the use of eDNA is therefore a reliable tool for the early detection of this “perfect invader”.
    • Customized medicine for corals

      Sweet, Michael; Peixoto, Raquel; Bourne, David; University of Derby; Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; IMAM-AquaRio – Rio de Janeiro Aquarium Research Center, Rio de Janeiro, Brazil; University of California; James Cook University, Townsville, QLD, Australia; Australian Institute of Marine Science, Townsville, QLD, Australia (Frontiers, 2019-11-13)
    • Compositional homogeneity in the pathobiome of a new, slow-spreading coral disease

      Sweet, Michael; Burian, Alfred; Fifer, James; Bulling, Mark; Elliott, David; Raymundo, Laurie; University of Derby; University of Guam (Springer Science and Business Media LLC, 2019-11-22)
      Coral reefs face unprecedented declines in diversity and cover, a development largely attributed to climate change-induced bleaching and subsequent disease outbreaks. Coral-associated microbiomes may strongly influence the fitness of their hosts and alter heat tolerance and disease susceptibility of coral colonies. Here, we describe a new coral disease found in Micronesia and present a detailed assessment of infection-driven changes in the coral microbiome. Combining field monitoring and histological, microscopic and next-generation barcoding assessments, we demonstrate that the outbreak of the disease, named ‘grey-patch disease’, is associated with the establishment of cyanobacterial biofilm overgrowing coral tissue. The disease is characterised by slow progression rates, with coral tissue sometimes growing back over the GPD biofilm. Network analysis of the corals’ microbiome highlighted the clustering of specific microbes which appeared to benefit from the onset of disease, resulting in the formation of ‘infection clusters’ in the microbiomes of apparently healthy corals. Our results appear to be in contrast to the recently proposed Anna-Karenina principle, which states that disturbances (such as disease) trigger chaotic dynamics in microbial communities and increase β-diversity. Here, we show significantly higher community similarity (compositional homogeneity) in the pathobiome of diseased corals, compared to the microbiome associated with apparently healthy tissue. A possible explanation for this pattern is strong competition between the pathogenic community and those associated with the ‘healthy’ coral holobiont, homogenising the composition of the pathobiome. Further, one of our key findings is that multiple agents appear to be involved in degrading the corals’ defences causing the onset of this disease. This supports recent findings indicating a need for a shift from the one-pathogen-one-disease paradigm to exploring the importance of multiple pathogenic players in any given disease.
    • 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.