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Research Highlights Archive

A selection of recent accomplishments from around our School drawn from the Disciplines of Botany, Geography, Geology, Zoology, Centre for the Environment, and the Trinity Centre for Biodiversity Research.

Research Highlights Archive from 2017


Genetic mutant can alter entire biological communities

Many bacterial species are highly social, adaptively shaping their local environment through the production of secreted molecules. A notable example is biofilm formation, whereby bacteria join together to form a dense aggregation. However, the impact of these social behaviours on complex communities is poorly understood. Research conducted by Dr. Ian Donohue and PhD student Deirdre McClean, along with collaborators in the Smurfit Institute of Genetics TCD and researchers in the University of Edinburgh, showed that bacterial social traits can reshape microbial communities. Specifically, we found that single-locus changes affecting biofilm formation phenotypes in Bacillus subtilis modify community structure to the same extent as loss of an apex predator and even to a greater extent than loss of B. subtilis itself. Our results from experimentally manipulated multitrophic microcosm assemblages also demonstrate the importance of social traits and their plasticity on the structuring of complex microbial communities, with major implications for our understanding of microbial ecology and disease aetiology. Moreover, they show that intraspecific genetic variability can be as important as strong trophic interactions in determining community dynamics. Microevolution may therefore be as important as species extinctions in shaping the response of microbial communities to environmental change.

The research was covered widely by the media including online news sites such as Nature World News, Irish Examiner,, and ScienceDaily.

A video summary of the research can be found here:


Bees prefer nectar containing pesticides

Bumble bee foraging on oilseed rape

Bumblebee foraging on oilseed rape in Ireland (Dara Stanley)

Neonicotinoids are systemic insecticides, currently banned for use on certain crops in the EU because of their potential negative effects on non-target organisms. Research conducted by Dr Jane Stout and PhD student Erin Jo Tiedeken, in collaboration with researchers at University of Newcastle in the UK, and published in Nature, has found that buff tailed bumblebees and honeybees cannot taste the three most commonly used neonicotinoid pesticides. In fact the research showed that the bees were attracted to nectar containing these common pesticides. This could increase their chances of exposure to high levels of pesticides. Previous studies have suggested that exposure of this kind can affect bees’ fitness. These findings imply that even if alternative food sources are provided for bees in agricultural landscapes where neonicotinoid pesticides are used, the bees may prefer to forage on the neonicotinoid‐contaminated crops. The research attracted global media attention including a commentary in Nature, and reports in Nature, New Scientist, Irish Times, Washington Post, New York Times, RTE and BBC as well as hundreds of other media sources worldwide.

At the same time, an independent scientific report prepared by EASAC concluded that there is significant evidence for negative effects associated with the widespread use of neonicotinoids on a wide range of non-target organisms that provide ecosystem services. Dr Stout was the Royal Irish Academy nominee to EASAC’s Working Group that prepared the report. She said: “Although much of the debate about neonicotinoids has focussed on honeybees, there is more and more evidence that widespread use of neonicotinoids could harm a range of organisms. This includes other pollinating insects, and ecosystem service providers like natural enemies of crop pests and soil organisms. For sustainable agricultural production, and maintenance of biodiversity in agricultural ecosystems, we need to produce food and manage pests in a way in which chemical treatments are used as a last resort – not in a prophylactic way.” This report gained worldwide media attention and has contributed to the European Food Safety Authority (EFSA) review on the controversial ban of neonicotinoids.

Kessler, S.C., Tiedeken, E.J., Simcock, K.L., Derveau, S., Mitchell, J., Softley, S., Stout, J.C. and Wright, G.A. 2015.  Bees prefer foods containing neonicotinoid pesticides. Nature, 521 (74-76) doi


Plastic carrier bags can smother marine life

Plastic bags

Plastic litter can smother marine life, dramatically reducing the numbers of organisms – and compromising the ecosystem services they provide – in coastal marshes. That is the key message to emerge from a collaborative study led by Dr Dannielle Green, an IRC-funded Research Fellow from Prof. Carlos Rocha’s Biogeochemistry Research Group in Geography.

The experimental study showed that in just nine weeks plastic bags smothered the surface of coastal sediment, preventing oxygen and nutrient flow, and blocking light. This caused a substantial reduction in the amount of microalgae beneath the bags. These tiny algae form the base of the food webs in these habitats, which means their proliferation is important for animals higher up the food chain, including worms and bivalves, which, in turn, are food for commercially important fish which feed within the marsh when the tide is in.

The same effects were there regardless of whether the plastic in question was biodegradable or not. While biodegradable plastics are produced because they are thought to be better for the environment because their persistence is shorter, our study suggests that the rate at which they break down may not be fast enough to have any meaningful advantage over conventional bags in marine habitats.

The paper was covered widely by the media including radio and online news sites such as The Journal and The Guardian.

Green, D.S., Boots, B., Blockley, D.J., Rocha, C. and Thompson, R. 2015. Impacts of Discarded Plastic Bags on Marine Assemblages and Ecosystem Functioning. Environ. Sci. Technol., 49: 5380–5389 doi

Trinity researchers find way to track volcano’s history

3d Volcano crystals

Every volcano has a story, but, until now, most of these stories were shrouded in mystery.

Trinity College Dublin Scientists have discovered how to prise volcanic secrets from magma crystals. These secrets include details of volcanic history, which explain global geography. Their discovery will help to better predict future eruptions of active volcanoes.

A team of geologists funded by SFI has optimised a laser ablation ICP-MS method to obtain the distribution of trace elements in magmatic crystals. Crystals record the history of magmatic processes taking place as they grow, therefore the trace element images or maps obtained with the new method can be used to prise pre-eruptive magma history and to hunt volcanic eruption triggers.

Full research: Ubide T, McKenna CA, Chew DM, Kamber BS (2015). High-resolution LA-ICP-MS trace element mapping of igneous minerals: in search of magma histories. Chemical Geology 409, 157-168, doi: 10.1016/j.chemgeo.2015.05.020.

Irish chronicles reveal links between cold weather and volcanic eruptions

Annals of Ulster

Medieval chronicles have revealed how volcanic eruptions affected the weather in Ireland up to 1500 years ago. An international research team, led by Francis Ludlow (who completed his PhD in TCD in 2010) and Mark Hennessy demonstrated a clear statistical relationship between cold episodes as recorded in the medieval Irish annals and volcanic eruptions as recorded in ice cores. It strengthens the evidence for volcanic forcing of cold events and also shows the value of documentary historical sources for the study of climate and weather.

This paper was covered widely in print and broadcast media including the BBC and was selected as a “Highlight of 2013” by Environmental Research Letters.

Ludlow, F., Stine, A.R., Leahy, P., Murphy, E., Mayewski, P.A., Taylor, D., Killen, J., Baillie, M.G.L., Hennessy, M., Kiely, G. (2013) Medieval chronicles reveal persistent volcanic forcing of severe winter cold events, 431–1649 CE. Environmental Research Letters, 8, 1–10.

The rise of a new mega geopolitical space: “South Space”

In 2013 Pádraig Carmody published “The Rise of the BRICS in Africa: The Geopolitics of South-South Relations” with Zed Books. The book explores, based in part on fieldwork in Zambia, the nature of the economic and political interactions between the BRICS (Brazil, Russia, India, China and South Africa) countries and Africa through case studies and other methods. Based on empirical and documentary analysis, Prof. Carmody argues that there is a new mega geopolitical space in formation which he calls “South Space”. As China’s role, in particular, has grown in importance in Africa, political elites have re-oriented their governance strategies to be more autonomous from Western-led institutions and donors to develop “hard shell sovereignty” in relation to human rights issues, for example. 

It is used as a core text in the M. Phil in African Studies at Cambridge University, for example, and also generated substantial media interest. Prof. Carmody was interviewed by The China Daily, European Centre for Development Management, Ozy and wrote a piece for The Guardian based on the book. He will give a keynote address to the inaugural Journal of Southern African Studies conference in Zambia in 2015 on the role of the BRICS in the region.

Prof. Carmody on fieldwork with Dr. Godfrey Hampwaye of the University of Zambia, funded by National Geographic.

Newly-discovered micro-organisms that improve important agronomic traits in barley

Brian Murphy with fungal endophytes and barley

A Botany research programme led by Trevor Hodkinson has recovered fungal micro-organisms from wild Irish relatives of barley and demonstrated that they confer significant benefits on cultivated barley. The research conducted by PhD student Brian Murphy has shown that these endophytes (fungi that live all or part of their lives within plant tissue without causing any obvious symptoms) have given 100% suppression of serious seed-borne barley pathogens and also increased yield and biomass under a number of abiotic stresses. A number of experiments were carried out in a controlled environment where barley plants were grown under individual and combined stresses. These stresses included nutrient, drought, heat and pathogen stress; in all cases the endophytes significantly improved at least two important agronomic traits in barley, such as number of shoots, grain yield and shoot biomass.  The endophytes have proven to be hyper-diverse and many potentially new species have been discovered. Field trials are planned to discover if these benefits translate to a more realistic agricultural situation. These endophytes have excited media and industry interest and informal collaborations with Irish and international specialists have been developed. The work has been featured in national television, radio and newspapers, and a feature article published in the international science magazine Scientific American.

Brian Murphy with fungal endophytes and barley.

Groundwater quality and groundwater influence on ecosystems

Groundwater quality and groundwater influence on ecosystems

Catherine Coxon is currently involved in several research projects on groundwater quality and groundwater influence on ecosystems.  These include a joint project with Teagasc on nitrogen transport and attenuation in hillslope systems in two agricultural catchments and a collaborative project with Jane Stout investigating the ecology and hydrology of dune slack ecosystems. Catherine also continues to work with Dr Katie Tedd on her Research Fellowship analysing data from the EPA national groundwater monitoring programme, with a recently published paper on spatial analysis of groundwater nitrate. Catherine has recently started a new project with colleagues in Zoology on development of an ecohydrology framework for setting environmental flow standards for Irish rivers.

Outputs from recently completed projects include two papers arising from a project on pesticides in Irish groundwaters (McManus et al. 2014, Journal of Environmental Monitoring and Assessment, 186, 7819-7836, and McManus et al. 2014, Molecules, 19, 20627-20649) and a paper on groundwater dependent terrestrial ecosystems accepted for publication in Biology and Environment with Visiting Research Fellow Dr Sarah Kimberley.

Toxic elements and waste-water treatment

Toxic elements and waste-water treatment

Nick Gray has set up a new laboratory in the Watts Building for water toxicity testing, with current work exploring the effects of pesticides on different freshwater trophic levels. This includes the use of a new macrophyte testing procedure, being used by postgraduate student Louise Esmonde.  Work is underway in deconstructing domestic wastewaters in order to identify where key toxicity elements arise and what components could be recovered or reused.  The use of natural microbial supplements to help enhance treatment is also currently being scoped through a range of undergraduate and masters projects, encouraging students to engage with the development of new research ideas. Work on a review of fixed film reactors in wastewater treatment is underway, and a recent paper has described how well vertical peat biofilters treat septic tank effluents. 
In a jointly authored book  Microbiology of Waterborne Diseases: Microbial Aspects and Risks published by Academic Press in February 2014  (659pp), Nick wrote seven chapters dealing with water disinfection and sterilization methods, as well as the effects of climate change on waterborne pathogens. He has also written a new book Facing up to Global Warming (350 pp) published by Springer (New York) which is due out in May 2015.

Gray, N.F. and Coady, J. (2015) Evaluation of full scale vertical peat biofilters for treatment of septic tank effluents, International Journal of Environmental Studies, 72, (1), 154-165.

School of Natural Sciences awarded multi-million € funding through Science Foundation Ireland (SFI) Centre

SFI announcment, Damien English, Balz Kamber, Mark Ferguson

SFI has announced 6-year funding for 5 research centres in areas of national economic importance. The School of Natural Sciences at TCD is proud to be a significant partner in one of the centres - iCRAG, the Irish Centre for Research in Applied Geosciences. iCRAG is a multi-university hub-and-spoke centre administered by University College Dublin. Two of the spokes, Raw Materials and Ground Water are led by TCD PI's Balz Kamber (Geology) and Laurence Gill (Civil Engineering).

Several researchers from the School of Natural Sciences (McClenaghan, Nicholas, Chew, C. Coxon, Rocha, Goodhue, Kamber) will conduct industry-collaboration research into a variety of questions such as: sediment provenance, continental rifting history, ore pathway finders, pyrite detection, groundwater discharge and quality, and high-tech metal recovery. The Centre will boost infrastructure and technical support in the School's expanding geochemical laboratory facilities and add to the growing number of the School's postdoctoral and postgraduate community. The research will further strengthen our ties with TCD alumni working as industry leaders across the globe.

Minister for Skills, Research and Innovation Damien English TD (left; holding a piece of Irish ore), Director General of Science Foundation Ireland Professor Mark Ferguson, (right) and Deputy Director of iCRAG Professor Balz Kamber (centre) at the SFI centers announcement.

Vultures acquire information on carcass location from scavenging eagles.

As social birds, vultures often rely on each other to find food. They frequently follow the descent of another individual in the hope that it has discovered a carcass. In an international piece of collaborative research, lead by Adam Kane and Andrew Jackson, that combined fieldwork in Kenya and mathematical modeling in Ireland, it was shown that vultures also take cues from scavenging eagles. Once an eagle lands at a carcass, the vultures soon follow and displace the smaller birds. The authors discuss the importance of ecosystem level management in light of these findings. Conservation actions need to focus on a higher level than that of an individual species given the tangled web of species interactions.

Kane, A., Jackson, A.L., Ogada, D.L., Monadjem, A. & McNally, L. 2014. Vultures acquire information on carcass location from scavenging eagles. Proceedings of the Royal Society of London B, 281 (1793) doi

Oxygenation of the Archean atmosphere: New paleosol constraints from eastern India

Hand sample 3.02 billion year old palaeosol

Quentin Crowley, Ussher Assistant Professor in Isotope Analysis and the Environment in the School of Natural Sciences at Trinity, is senior author of a paper published in the world's top-ranked Geology journal, Geology. Working with Ph.D. student Kyle Heron, Professors Joydip Mukhopadhyay and Gautam Ghosh and other colleagues from Presidency University in Kolkata, India, their research found evidence for chemical weathering of rocks leading to soil formation that occurred in the presence of oxygen at least 3.02 billion years ago. Such substantial levels of oxygen could only have been produced by organisms capable of oxygenic photosynthesis. The early Earth was very different to what we see today. Our planet's early atmosphere was rich in methane and carbon dioxide and had only very low levels of oxygen. The widely accepted model for evolution of the atmosphere states that oxygen levels did not appreciably rise until about 2.4 billion years ago. This 'Great Oxidation Event' event enriched the atmosphere and oceans with oxygen, and heralded one of the biggest shifts in evolutionary history. Micro-organisms were certainly present before 3.0 billion years ago but they were not likely capable of producing oxygen by photosynthesis. Up until very recently however, it has been unclear if any oxygenation events occurred prior to the Great Oxidation Event and the argument for an evolutionary capability of photosynthesis has largely been based on the first signs of an oxygen build-up in the atmosphere and oceans.

Professor Crowley concluded: "Our research gives further credence to the notion of early and short-lived atmospheric oxygenation. This particular example is the oldest known example of oxidative weathering from a terrestrial environment, occurring about 600 million years before the Great Oxidation Event that laid the foundations for the evolution of complex life."

Oxygenation of the Archean atmosphere: New paleosol constraints from eastern India. 2014. Geology. Joydip Mukhopadhyay, Quentin G. Crowley*, Sampa Ghosh, Gautam Ghosh, Kalyan Chakrabarti, Brundaban Misra, Kyle Heron, Sankar Bose. DOI

Photos are available at:

OXYGENATION SYMOPSIUM: Quentin Crowley recently hosted a symposium on this theme, which was funded by the Irish Research Council, with a contribution from the School's research fund.

Breakthroughs in Understanding Grassland Ecosystems on a Global Scale

cover image of the book, Ascaris, the neglected parasite.

Fertiliser reduces plant diversity and can increase variability in grassland production, but in fertilized grasslands grazers help enhance diversity by ensuring dominant species don't steal all the sunlight. In two globally collaborative studies, published in Nature reporting the effects of fertilization and grazing on plant diversity and stability of grassland production, scientists used the Nutrient Network, or 'NutNet', to help predict how grasslands around the world will respond to a changing environment. Fertilisation reduces plant diversity as some species are able to take advantage of higher nutrient availability to grow quickly and shade out smaller or slower growing species. If grazers remove some of this extra biomass however the availability of light to smaller and slower growing species can be maintained. Fertilisation of grasslands also breaks down the link between plant diversity and stable biomass production so that higher diversity sites no longer provide more stable biomass production than lower diversity sites. NutNet is a grass-roots campaign supported by scientists who volunteer their time and resources. There are now 75 sites around the world that are run by more than 100 scientists. Professor Yvonne Buckley has been involved in NutNet since 2007 and will soon establish the first Irish site to add to NutNet's growing catchment area.
For more information please contact Yvonne Buckley

Hautier et al. In press. Eutrophication weakens stabilizing effects of diversity in natural grasslands. Nature. Available Online doi

Borer et al. In press. Herbivores and nutrients control grassland plant diversity via light limitation. Nature. Available Online doi

Ascaris, a parasite of global significance but why so neglected?

cover image of the book, Ascaris, the neglected parasite.

“Ascaris the neglected parasite” by Professor Celia Holland, is a call to arms for renewed research effort into ascariasis. This disease has been described by Peter Hotez, the guru of neglected tropical diseases (NTDs), as the ultimate NTD owing to its devastating impact on child health and the general lack of awareness of its true global importance. As a soil transmitted parasite, it results in chronic morbidity and presents an enormous challenge in regions of the world dominated by inadequate sanitation and poverty. The lack of a rodent animal model, in which the parasite completes its life cycle in a manner similar to humans, is an undoubted disadvantage as is the declining numbers off investigators that make Ascaris their focus. Prof Holland edited this book by drawing chapters from the World’s experts. It provides a blueprint of how a single parasite entity can engender interest in basic biology, clinical science, veterinary science, public health and epidemiology. One particular strength of the book is the elegant illustration of how quantitative biology can contribute to public health policy.

Holland, C.V. 2013. Ascaris: The Neglected Parasite. Academic Press. ISBN 978-0123969781

Informing Food Futures through CONSENSUS

photograph of a poster whose title reads "tell us what you think".

Food security is an issue of global concern. However, solutions are traditionally focused on agricultural intensification, which leads to environmental, social and economic challenges. Yet, the other side of the food equation, the practice of eating, remains understudied. Trinity Geographers Prof. Anna Davies, Drs. Laura Devaney and Ruth Doyle recently completed a workpackage in the CONSENSUS project which aimed to rebalance the food futures debate. They designed and implemented novel co-design experiments to think through the question of eating more sustainably in the future. Key actors along the length of the food chain from public, private and civil society sectors were brought together to develop alternative scenarios for more sustainable food consumption. Following the publication of this work in Eurochoices (Davies, 2013), Prof. Davies was invited to participate in an OECD workshop in Paris on long-term scenarios for food and agriculture, presenting on ‘Challenges in food consumption practices towards 2050’. This workshop will culminate in a final report on policy choices for feeding the world of tomorrow, highlighting the centrality of the CONSENSUS research findings in global food and agricultural debates.

Davies, A.R. (2013) Food Futures: Co-designing Sustainable Eating Practices for 2050, Eurochoices. Summer 2013, vol. 12 (2), 4-11 doi

Forests Buffer the Effects of Climate Change on Plants

photograph looking up into the canopy of a forest

Collaborative international research involving Daniel Kelly, Fraser Mitchell and Miles Newman with researchers in Europe and the US scientists has shown that cool forest microclimates limit the effects of climate change on plants beneath the canopy. The work, published in the Proceedings of the National Academy of Sciences shows that species that are better adapted to relatively warm temperatures are less dominant in these environments.  An unprecedented 1400 vegetation surveys from European and North-American ancient deciduous forests were compiled. This revealed that ‘warm-adapted’ species, such as common ivy, have become considerably more common than they were 35 years ago, but under the forest canopy cooler temperatures are limiting their spread. It is thus recommended that forests should be preserved as safe refuges for cold-adapted plants that are struggling in a warmer world. It is interesting to note that the Irish data contributed to this international investigation provide the strongest support for the overall conclusion that dense forest canopies damped the impact of global warming. This implies that the flora in Irish woodland is most vulnerable to the impacts of global warming if the tree canopy cover is not maintained. The principal threat to maintaining canopy cover is the inability of trees to generate due to high grazing pressure and this has been identified as a significant issue in woodland across the state.

De Freene, P. et al. 2013. Microclimate moderates plant responses to macroclimate warming. Proc Nat Acad Sci 110(46) pp 18561-18565. doi

Time is in the eye of the beholder

photo image of close up of a human eye with a clock set over the iris

An international collaboration led by Dr Andrew Jackson and PhD student Kevin Healy including researchers from the University of Edinburgh and the University of St. Andrews has shown that animals’ ability to perceive time is linked to their pace of life. The study which was published in the leading international journal Animal Behaviour, showed that small-bodied animals with fast metabolic rates, such as some birds, perceive more information in a unit of time, hence experiencing time more slowly than large bodied animals with slow metabolic rates, such as large turtles. The researchers took advantage of this phenomenon to explain the observed variation in time perception across a broad range of animals, showing that animals that would be expected to be agile possess the most refined ability to see time at high resolutions.

Healy, K., McNally, L., Ruxton, G.D., Cooper, N. & Jackson, A.L. 2013. Metabolic rate and body size linked with perception of temporal information. Animal Behaviour, 86(4), 685-696 doi

Effects of energy crops on biodiversity and ecosystem service

image of a field of miscanthus plants

Recent research as part of the SIMBIOSYS project, led by Jane Stout in the School of Natural Sciences and Trinity Centre for Biodiversity Research, has quantified the effects of growing bioenergy crops on biodiversity and ecosystem services in Ireland. PhD student, Jesko Zimmermann and Prof Mike Jones, in their recent paper in Global Change Biology Bioenergy, showed that even just two years after planting Miscanthus (a fast growing perennial grass grown for biofuel), a significant amount of carbon was already sequestered into soils.  Furthermore, contrary to expectation, planting Miscanthus did not lead to significant losses in existing soil organic carbon stocks. Another PhD student, Dara Stanley, working with Jane Stout, investigated the effects of energy crops on pollinators and pollination and found that exclusion of pollinators from oilseed rape resulted in approximately 30% decrease in seed number and weight, equivalent to nearly €4 million per annum (published in Journal of Insect Conservation). Furthermore, Dara’s work showed that a wide range of pollinating insects use bioenergy fields (published in Journal of Applied Ecology) and that bees from more than 800 bumblebee colonies are attracted to individual oilseed rape fields (published in PLoS ONE).

Geology at the sub-microscopic scale

image of a field of a microscope view of a crystal

At the atomic level, the behaviour of chemical elements in solid matter is governed by the exact structure of the surrounding crystal. The quantification of these effects is at the forefront of geochemical research, to which TCD's Geology PIs are contributing with recent publications. Dr. Quentin Crowley was part of a team that demonstrated, for the first time, how the apparent age of zircon from highly deformed rocks can be affected by distortion of crystal lattice structures. Meanwhile, Prof. Balz Kamber and his PhD student Kirk Ross published the first empirical test of the widely used crystal lattice strain model for incorporation of the energy critical rare earth elements into pyroxene. Finally, Dr. David Chew and colleagues developed a new analytical approach to determine the chlorine content of apatite, which exerts critical control over the temperature at which fission tracks are erased. Collectively, these contributions demonstrate the convergence of geochemistry and nanoscience.

MacDonald, J.M., Wheeler, J., Harley, S.L., Mariani, E., Goodenough, K.M., Crowley, Q., Tatham, D. (2013). Lattice distortion in a zircon population and its effects on trace element mobility and U-Th-Pb isotope systematics: examples from the Lewisian Gneiss Complex, northwest Scotland, Contributions to Mineralogy and Petrology, 166, 21-41.
Ross, K., Kamber, B.S. and McDonald, A. M. (2013): An empirical test of the crystal lattice strain model for rare earth element partitioning into clinopyroxene. Chemical Geology, 340, 139-150.
Chew, D.M., Donelick, R.A., Donelick, M.B., Kamber, B.S., and Stock, M.J. (2013): Apatite chlorine concentration measurements by LA-ICPMS. Geostandards and Geoanalytical Research.