69 research outputs found
Hubas-prog/ASSEMBLE-MICROBE: Second release
No full textThis is the second release of the Supp. Mat. of article entitled "Identity and sequence: The effect of multiple stressors on microphytobenthos assemblages" by James E V Rimmer, Cédric Hubas, Adam Wyness, Bruno Jesus, Morgan Hartley, Andrew J Blight, Antoine Prins, David M Paterson. This new release includes a readme file with indications about R scripts and Script correspondance to help the reader
Hubas-prog/ASSEMBLE-MICROBE: Initial release
No full textThis is the initial release of the Supp. Mat. of article entitled "Identity and sequence: The effect of multiple stressors on microphytobenthos assemblages" by James E V Rimmer, Cédric Hubas, Adam Wyness, Bruno Jesus, Morgan Hartley, Andrew J Blight, Antoine Prins, David M Paterso
The End of Free College in England: Implications for Quality, Enrolments, and Equity
No full textAssistant Professor Richard Murphy, Associate Professor Judith Scott-Clayton and Dr Gill Wyness show that England’s move to a high tuition fee system has led to increased quality, enrolments and equity in higher education.
The paper looks at the consequences of tuition fees in England, now among the highest in the world, from their introduction in 1998 up to the present day.
The findings show that over the last two decades tuition fees have led to substantial increases in funding per head, while enrolments have continued to rise, and the participation gap between rich and poor students has narrowed.
In contrast to the 1980s and 1990s, which also saw increases in university enrolments, the most rapid growth in participation rates since the introduction of fees has been among the lowest income groups.
The researchers suggest that this may be due to the fact that significant increases in the cost of going to university have been accompanied by corresponding increases in student aid. This is supported by evidence showing a decline in part-time students, who are for the most part unable to access this aid, during the same time period.
In contrast to other countries with high tuition fees, England’s system of income-contingent loans allows students to safely borrow against their future incomes and means that university is free at the point of entry. The poorest students in England can now access £8,500 per year in aid, compared to less than £5,000 per year in the period immediately before tuition fees.
The most notable trend taking place in the years since the introduction of fees has been the dramatic increase in investment in the sector, according to the study. The findings show that student funding per head fell to a historical low in 1999 (£6,500 per student) but has since recovered to levels seen at the beginning of the 1990s (around £9,700 per student).
The researchers argue that this evidence highlights one of the key challenges facing a state-funded, expanding higher education system: insufficient resources.
The researchers point out that a shortcoming of England’s income contingent loans system is that government bears the full risk of non-repayment while the university bears none. This means that universities have little incentive to vary prices to reflect quality. A further issue is that the system is still poorly understood by students.
Dr Gill Wyness, co-author of the study, said: ‘The income-contingent loan system in place in England has really helped to moderate the impact of rising tuition. It keeps university free at the point of entry, and provides students with comparatively generous assistance for living expenses, while protecting low earning graduates from the risk of high repayments.
An agent-based model that simulates the spatio-temporal dynamics of sources and transfer mechanisms contributing faecal indicator organisms to streams. Part 2: Application to a small agricultural catchment
No full textSoftware and data availability The source code for MAFIO as used in this work is available via the University of Aberdeen PURE repository: https://doi.org/10.20392/66f74663-ece3-4a52-8bed-f0cf52d0831a. The source code for EcH2O-iso is available at: https://bitbucket.org/sylka/ech2o_iso/src/master_2.0/. The Tulloch Burn datasets used in this study are available from the lead author on request. Acknowledgments Funding for this work from the Scottish Government’s Hydro Nation Scholars Programme is gratefully acknowledged. Many thanks to Audrey Innes, Jonathan Dick, Claire Tunaley and Bernhard Scheliga for their assistance in analysing the isotope samples. In addition, thanks to Allan Sim, Duncan White and, in particular, Claire Abel and Adam Wyness for instruction and training on microbiological sampling and analysis techniques. Simulations with EcH2O-iso and MAFIO were undertaken on the Maxwell high performance computing cluster funded by the University of Aberdeen. Sylvain Kuppel and Aaron Smith are thanked for their assistance in troubleshooting occasional issues with EcH2O-iso.Peer reviewe
The influence of sediment characteristics on the abundance and distribution of E.coli in estuarine sediments
No full textMicrobiological water quality monitoring of bathing waters does not account for faecal bacteria in sediments. Intertidal deposits are a significant reservoir of faecal bacteria and this indicates there is a risk to human health through direct contact with the sediment, or through the resuspension of bacteria to the water column.
This project investigated factors influencing the relative abundance of faecal indicator organisms (FIOs) in intertidal estuarine sediments. The effects of physical, biogeochemical and biological sediment characteristics, environmental variables and native microbial communities were explored through field campaigns on the Ythan and Eden estuaries, Scotland. The contributory role of sediments to adverse water quality was investigated by combining FIO abundance and measurements of sediment stability. The importance of strain and sediment characteristics in the adhesion of E. coli to suspended sediments was also examined using laboratory experiments.
E. coli concentrations up to 5.9 log₁₀ CFU 100 g dry wt⁻¹ were observed, confirming that intertidal sediments are an important reservoir of faecal bacteria. The variability of E. coli abundance in estuarine sediments was successfully explained with multiple stepwise linear regression (Adjusted R² up to 87.4) using easily-obtainable measurements of sediment characteristics and environmental variables, with variability most heavily influenced by salinity and particle size gradients. Native microbial community population metrics and community constituent composition correlated with environmental gradients, but did not influence FIO abundance. The amount of E. coli adhering to suspended sediments ranged from 0.02 to 0.74 log₁₀ CFU ml⁻¹, and was dependant on strain characteristics and sediment type rather than zeta potential, with higher cell-particle adhesion at 2 and 3.5 PSU than 0 and 5 PSU.
Monitoring of sediment characteristics will lead to more informed bathing water quality advisories to protect public health. Future research should focus on applying the findings here to the modelling of bacterial fate and transport on a catchment scale
Children's participation and intergenerational dialogue : Bringing adults back into the analysis
No full textWithin the field of children’s participation there has been a shift from adults mediating children’s worlds to children themselves becoming the sole interpreters of their own standpoints. In the process this has sometimes led to the marginalisation of adults’ perspectives on and contributions to children’s participation. In this article the author argues that analyses of children’s participatory roles need to take account of the form and nature of children’s relationships with adults. Drawing on the notion of intergenerational dialogue the article explores a range of political and global themes that highlight the participatory roles of children and their interdependence on adults
Spatial variability of microbial communities and salt distributions across a latitudinal aridity gradient in the Atacama Desert
No full textThis research was funded by European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement 678812) (to MWC) for 2017 sampling and various geochemical characterizations, and John Templeton Foundation (Grant Agreement 60501) (to AJW) for assistance with sequencing and bioinformatics. J.S. also acknowledges support from the China Scholarship Council (CSC).Over the past 150 million years, the Chilean Atacama Desert has been transformed into one of the most inhospitable landscapes by geophysical changes, which makes it an ideal Mars analog that has been explored for decades. However, a heavy rainfall that occurred in the Atacama in 2017 provides a unique opportunity to study the response of resident extremophiles to rapid environmental change associated with excessive water and salt shock. Here we combine mineral/salt composition measurements, amendment cell culture experiments, and next-generation sequencing analyses to study the variations in salts and microbial communities along a latitudinal aridity gradient of the Atacama Desert. In addition, we examine the reshuffling of Atacama microbiomes after the rainfall event. Analysis of microbial community composition revealed that soils within the southern arid desert were consistently dominated by Actinobacteria, Chloroflexi, Proteobacteria, Firmicutes, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Acidobacteria, and Verrucomicrobia. Intriguingly, the hyperarid microbial consortia exhibited a similar pattern to the more southern desert. Salts at the shallow subsurface were dissolved and leached down to a deeper layer, challenging indigenous microorganisms with the increasing osmotic stress. Microbial viability was found to change with aridity and rainfall events. This study sheds light on the structure of xerotolerant, halotolerant, and radioresistant microbiomes from the hyperarid northern desert to the less arid southern transition region, as well as their response to changes in water availability.Peer reviewe
Towards a Standardized Operating Procedure for eDNA-Based Biomonitoring in Coastal Marine Salmon Aquaculture
No full textThe marine aquaculture industry and regulators are in the process of implementing environmental DNA (eDNA) metabarcoding of microbial communities for compliance monitoring. This requires standardization of sampling, laboratory, and data analysis protocols. Towards this goal, we in this study completed two further milestones using samples collected from two Scottish salmon farms: (i) We tested the effect of using two different PCR protocols (i.e., different DNA polymerases, master mixes, and annealing temperatures), which are frequently being used in eDNA biomonitoring of aquaculture installations, for the amplification of the taxonomic marker gene (V3-V4 hypervariable region of the bacterial 16S rRNA gene). (ii) We quantified sampling background noise obtained from eDNA samples and statistically compared results with the sampling bias observed in macrofaunal samples from the same source sediments. We detected differences in bacterial community structures resulting from the performance of different PCR protocols, profoundly influencing the interpretation of biomonitoring results. Furthermore, we found that sampling-induced errors for eDNA samples were similar to errors for macrofaunal samples collected according to compliance monitoring protocol (~25% variability in both cases). Finally, we showed that within-grab variances of microbial community structures were in the same order of magnitude (less than 10× difference in all cases) as the one obtained from replicate grabs collected from the same locale (impact category). Based on our findings, we suggest using a consistent PCR protocol for biomonitoring efforts to improve the comparability of results, especially when different service providers are conducting the biomonitoring. We propose a sampling scheme to be considered in eDNA biomonitoring that includes taking three replicate grabs at each locale, with one replicate sample from each grab. This minimizes sampling-induced errors and makes upcoming eDNA-based monitoring results comparable with previous compliance monitoring results obtained from macrofaunal data
A DNA-based investigation of endolithic community succession on shells of the limpet Patella depressa Pennant 1777
No full textBiotic and abiotic calcium carbonate structures are used as a substrate by bioeroding organisms, or euendoliths, worldwide. Euendoliths can have serious ecological effects on living hosts, and with global increases in ocean acidification and warming, the efficiency of erosion by marine euendoliths is likely to increase. Here, we used growth curve data for the limpet Patella depressa and 16S rRNA sequencing to explore succession in the endolithic community on the shells of P. depressa throughout its range across Great Britain. Limpet age correlated well with the extent of erosion within sites, but differed among sites, with those at the centre of the host range showing greater erosion when corrected for age. Alpha-diversity and richness of cyanobacteria decreased with the extent of erosion, particularly during the earlier stages of erosion. A decrease in the accumulation rate of Amplicon Sequence Variants (ASVs) occurred at around 80 % of cumulative ASVs, at a shell age of between 1.4 and 2.7 years. Cyanobacterial community composition differed among the shells from the different sites, but despite these differences, there were no discernable patterns in the abundance of specific taxa that were associated with limpet age or the extent of erosion. The results revealed that, when examined at a high taxonomic resolution, cyanobacterial community succession is more complex than previously thought, and may be site-specific. However, the trends observed indicate that cyanobacterial community succession occurs on calcifying organisms in vivo, with a shift towards a climax community after 1.4–2.7 years for P. depressa
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