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Recent Publications

Recent Publications (highlights from across IBES)

Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil.
Lehtovirta-Morley LE, Stoecker K, Vilcinskas A, Prosser JI, Nicol GW.
Proc Natl Acad Sci U S A. 2011 Sep 6. [Epub ahead of print]

  • Nitrification rates in acidic soils (pH < 5.5), which comprise 30% of the world’s soils, equal or exceed those of neutral soils.
  • Paradoxically, all ammonia oxidizers cultivated over the last 120 years demonstrate little or no growth below pH 6.5.
  • This paper describes the discovery and characterisation of a soil archaeon that represents the world’s first obligately acidophilic ammonia oxidiser and the first ammonia oxidiser cultured that cannot grow at neutral pH.
  • To recognise the importance of the site from which the soil was obtained, and the university at which it was first cultivated, the organism has been named Nitrosotalea devanaterra, which mean an ammonia oxidising ‘rod’ from soil in Aberdeen, incorporating Devana, the Roman name for Aberdeen.
A novel minicollagen gene links cnidarians and myxozoans
Jason W. Holland, Beth Okamura, Hanna Hartikainen, and Chris J. Secombes
Proc. R. Soc. B, 2011 278:546-553

A molecular switch for photoperiod responsiveness in mammals.
Dardente H, Wyse CA, Dupre SM, Birnie MJ, Loudon ASIL, Lincoln GA, Hazlerigg DG
Current Biology, 2010, 20:2193-2198.

  • We link the circadian clock to TSH-dependent seasonal biology through the transcriptional coactivator, Eya3. We now show that Eya's role is to drive up the expression of TSHb, and hence that it is the lynchpin of the vertebrate photoperiodic response.
  • The model that emerges amounts to a molecular "external coincidence timer" - a concept postulating that day length measurement involves the circadian system. Eya3 is circadianly controlled AND directly suppressed by darkness. This is the "coincidence timer", which is the key to photoperiodic decision making.
  • We also describe comparative differences in the sensitivity of the D-element in the bTSH promoter, which correlate with differential reliance on photoperiod for seasonal control. Hence, following on from describing a molecular pathway linking the circadian clock to seasonal biology, we show how simple variations in a classic clock-controlled DNA response element might lead to evolved differences in seasonal biology.
  • Link to University of Aberdeen news. (2nd Dec 2010)

Antipodean white sharks on a Mediterranean walkabout? Historical dispersal leads to genetic discontinuity and an endangered anomalous population.
Chrysoula Gubili, Rasit Bilgin, Evrim Kalkan, S. Ünsal Karhan, Catherine S. Jones, David W. Sims, Hakan Kabasakal, Andrew P. Martin, and Leslie R. Noble
Proc. R. Soc. B published online before print November 17, 2010, doi:10.1098/rspb.2010.1856

  • Great white sharks found in the Mediterranean were originally from Australia.
  • A navigational error, possibly by a few pregnant females, around 450,000 years ago during a time of global climate change, probably prompted them to take a ‘wrong turn’. 
  • Link to University of Aberdeen news. 
  • Link to BBC News

Heritability of female extra-pair paternity rate in song sparrows (Melospiza melodia)
Jane M. Reid, Peter Arcese, Rebecca J. Sardell and Lukas F. Keller,
Proceedings of the Royal Society B, Published online before print October 27, 2010, doi: 10.1098/rspb.2010.1704

  • "Promiscuous birds can blame it on their genes" - Planet Earth online, news, from the Natural Environment Research Council
In vivo differential effects of fasting, re-feeding, insulin and insulin stimulation time course on insulin signaling pathway components in peripheral tissues.
Agouni A, Owen C, Czopek A, Mody N, Delibegovic M.
Biochem Biophys Res Commun. 2010 Oct 8;401(1):104-11.
  • We examined the effects of fasting duration on insulin receptor phosphorylation and that of its downstream components in insulin-sensitive peripheral tissues skeletal muscle, liver and fat of mice.
  • We determined that a short physiological fast (5 hours) results in similar insulin-stimulated response in phosphorylation events compared to overnight fast/starvation. In addition to insulin, refeeding led to a robust phosphoryation of p70 S6 kinase substrate S6 but the absence of an equally strong activation of the insulin receptor.
  • A time course of insulin-stimulated phosphorylation revealed divergent events in different insulin-sensitive tissues.
  • These studies will aid in the investigation of impaired insulin action in mouse models of obesity, insulin resistance and type-2 diabetes.

Species Interactions in a Parasite Community Drive Infection Risk in a Wildlife Population
Sandra Telfer, Xavier Lambin, Richard Birtles, Pablo Beldomenico, Sarah Burthe, Steve Paterson, and Mike Begon
Science 8 October 2010: 243-246.

  • We live under constant assault from a variety of pathogens. Pathogen exposure will be more or less harmful depending on host factors, including immune status and the presence of co-infecting pathogens.
  • In a time-series study of wild voles and four pathogens, co-infection had a larger effect on disease than any other factor. For example, infection with cowpox virus increased susceptibility and prolonged bacterial co-infections.
  • Conversely, an ongoing infection with the bacterium Anaplasma reduced the rodents' susceptibility to the protozoan Babesia. In turn, chronic infection with Babesia limited susceptibilityto the bacterium Bartonella.
  • Perspective in Science magazine.
  • Planet Earth online - news, from the Natural Environment Research Council

Autotrophic ammonia oxidation by soil thaumarchaea
Zhang, L., Offre, P.O., He, J.-Z., Verhamme, D.T., Nicol, G.W., and Prosser, J.I. Proceedings of the National Academy of Sciences USA. 2010. 107: 17240–17245

  • Ammonia oxidation, a critical step in the global nitrogen cycle, was thought to be performed by autotrophic bacteria until the recent discovery of archaeal ammonia oxidizers. However, there remains uncertainty and controversy regarding which organisms are responsible for oxidising ammonia in terrestrial systems.
  • The results presented in this paper provide direct evidence for a role for archaea in soil ammonia oxidation and demonstrate, for the first time, autotrophic growth of ammonia oxidising archaea in soil.

Starvation alters the liver transcriptome of the innate immune response in Atlantic salmon (Salmo salar)
Samuel A.M. Martin, Alex Douglas, Dominic F Houlihan, Christopher J Secombes BMC Genomics 2010, 11:418 (5 July 2010)

  • The transcriptional response of genes in the liver of Atlantic salmon following an acute bacterial infection is affected by their previous feeding regime.
  • However, starved fish display a significantly reduced innate immune response.

Environmental context explains Lévy and Brownian movement patterns of marine predators
Nicolas E. Humphries, Nuno Queiroz, Jennifer R. M. Dyer, Nicolas G. Pade, Michael K. Musyl, Kurt M. Schaefer, Daniel W. Fuller, Juerg M. Brunnschweiler, Thomas K. Doyle, Jonathan D. R. Houghton, Graeme C. Hays, Catherine S. Jones, Leslie R. Noble, Victoria J. Wearmouth, Emily J. Southall & David W. Sims.
Nature 2010 465:1066–1069

  • What is the best way for predators to find food when prey is sparse and distributed unpredictably?
  • Theory predicts that in such circumstances predators should adopt a Lé-flight strategy, in which short exploratory hops are occasionally interspersed with longer trips. When prey is abundant, simple Brownian motion should suffice.
  • Now, analysis of a large data set of marine predators establishes that animals do indeed adopt Lévy-flight foraging when prey is sparse, and Brownian episodes when prey is abundant.

See also: Nature Editor's summary, News and Views by Viswanathan & University of Aberdeen news

Sub-surface hotspots in shallow seas: fine-scale limited locations of top predator foraging habitat indicated by tidal mixing and sub-surface chlorophyll
Beth. E. Scott, J. Sharples, O. N. Ross, J. Wang, G. J. Pierce, C. J. Camphuysen
Marine Ecology Progress Series (2010) 08:207-226

  • In this study we set out to define similarities and differences of the foraging habitats of a range of seven species of top predators (seabirds and marine mammals) in a shallow sea region.

  • The occurrence of foraging habitats overall were extremely patchy with the best indicator of the probability of presence and abundance of individual species was found to be a static habitat variable describing levels of tidal stratification. The other common habitat characteristics were areas with high concentrations of sub-surface chlorophyll and high variance in bottom topography.

  • These 'hotspots' may be the only locations where the majority of predator-prey interactions actually occur and represent a newly-identified class of spatially important locations that are not readily identifiable from surface characteristics.

Maximal heat dissipation capacity and hyperthermia risk: neglected key factors in the ecology of endotherms
John R. Speakman and Elzbieta Król
Journal of Animal Ecology (2010) 79 (4):726 - 746

  • The traditional view of energy in ecology is that it is a limited resource – either because there is insufficient energy in the environment, or the acquisition and distribution systems in the animal restrict its availability (the metabolic theory of ecology).
  • This ‘field altering paper’ (quoted from Journal of Animal Ecology website) suggests that in many cases energy is not a limiting factor but rather animals (particularly endotherms) are constrained by their capacity to dissipate heat.
  • This new view of animal energetic forces a reassessment of whole areas of ecophysiology – such as the patterns of investment in reproduction, Bergmann’s law, limitations on performance and the scaling of maximal energy metabolism in relation to body mass.

Intron-Containing Type I and Type III IFN Coexist in Amphibians: Refuting the Concept That a Retroposition Event Gave Rise to Type I IFNs
Zhitao Qi, Pin Nie, Chris J. Secombes, and Jun Zou
J Immunol 2010 184: 5038-5046.

  • Interferons are instrumental to vertebrate antiviral defence.
  • In this paper, we have demonstrated for the first time that intron containing type I and III genes diverged relatively early in vertebrate evolution, and at least by the appearance of early tetrapods.
  • Origin of the intron lacking type I interferon genes in modern vertebrates has been discussed.
Marine biodiversity–ecosystem functions under uncertain environmental futures.

Mark T. Bulling, Natalie Hicks, Leigh Murray, David M. Paterson, Dave Raffaelli, Piran C. L. White, and Martin Solan
Philosophical Transactions of the Royal Society, B. 2010 365:2107-2116

  • The roles of two important climate change variables and biodiversity loss on nutrient cycling in a marine mud flat community was examined.
  • We find that higher tempertaures and greater concentrations of carbon dioxide have negative impacts on nutrient cycling
  • Interactions between temperature and anticipated carbon dioxide levels mean that reliably predicting the environmental consequences of future climate change will not be straightforward.

Factors Affecting Benthic Impacts at Scottish Fish Farms.
Mayor DJ, Zuur AF, Solan M, Paton GI, Killham K.
Environ Sci Technol. 2010, 44 (6), pp 2079–2084

  • Lead researcher, Dr Daniel Mayor from the Institute’s Oceanlab examined how the size of a fish farm relates to the size of its ‘environmental footprint’.
  • They analysed data from 50 Scottish fish farms and found that larger fish farms do not necessarily have a greater effect on the sea floor than smaller fish farms.
  • Link to University of Aberdeen news

Hadal Trenches: the ecology of the deepest places on Earth.
Jamieson, A.J., Fujii, T., Mayor, D.J., Solan, M. & Priede, I.G.
Trends in Ecology and Evolution. 2010, 25 (3) 190-197

  • The hadal zone (6000-10,000m) represents the deepest habitat on Earth. 
  • In this paper we review our current understanding on the ecological function of this extreme environment and the roles of species therein.
  • Go to NERC - Planet Earth website  and search for "hadal" to see articles and multimedia from the expeditions leading to this paper.

Do rabbits eat voles? Apparent competition, habitat heterogeneity and large-scale coexistence under mink predation.
Oliver M, Luque-Larena JJ and Lambin X.
Ecol Lett. 2009 Nov;12(11):1201-9.


Ribosomal protein S6 kinase 1 signaling regulates mammalian life span.
Selman C, Tullet JM, Wieser D, Irvine E, Lingard SJ, Choudhury AI, Claret M,
Al-Qassab H, Carmignac D, Ramadani F, Woods A, Robinson IC, Schuster E, Batterham RL, Kozma SC, Thomas G, Carling D, Okkenhaug K, Thornton JM, Partridge L, Gems D, Withers DJ.
Science. 2009 Oct 2;326(5949):140-4. 

Liparid and Macrourid fishes of the hadal zone: In situ observations of activity and feeding behaviour.
Jamieson, AJ, Fujii, T, Solan, M., Matsumoto, AK, Bagley, PM & Priede, IG Proceedings of the Royal Society Part B. 2009, 276: 1037-1045

  • The presence of fish at depths greater than 6000m has been known since the 1950s however no one has, until now, ever seen them alive. 
  • Here we describe the first ever live observations fish species deeper than 6000 m and discuss their behaviour and physiology.

Analogous aquatic and terrestrial food webs in the high Arctic: The structuring force of a harsh climate
René van der Wal, Dag O. Hessen
Perspectives in Plant Ecology, Evolution and Systematics (2009) 11, 3: 231-240


Can managers inform models? Integrating local knowledge into models of red deer habitat use
R. J. Irvine, S. Fiorini, S. Yearley, J. E. McLeod, A. Turner, H. Armstrong, P. C. L. White, R. van der Wal
Journal of Applied Ecology (2009) 46: 344-352.


Greenhouse gas mitigation in agriculture.
Smith, P., Martino, D., Cai, Z., Gwary, D., Janzen, H.H., Kumar, P., McCarl, B., Ogle, S., O’Mara, F., Rice, C., Scholes, R.J., Sirotenko, O., Howden, M., McAllister, T., Pan, G., Romanenkov, V., Schneider, U., Towprayoon, S., Wattenbach, M. & Smith, J.U.
Philosophical Transactions of the Royal Society, B. 2008, 363, 789-813.

  • Food production accounts for up to 30% of all human emissions of greenhouse gases, the gases that cause climate change.
  • This paper makes the first global assessment of the potential to reduce greenhouse gas emissions from agriculture.
  • The paper formed the basis of the chapter on greenhouse gas reduction possibilities in agriculture (which I led) in the Intergovernmental Panel on Climate Change's (IPCC) last assessment report on climate change.
  • This IPCC was awarded the Nobel Peace Prize for this and previous work in 2007.

The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria.
Graeme W. Nicol, Sven Leininger, Christa Schleper, James I. Prosser
Environmental Microbiology 2008 10: 2966-2978

  • There has been a long-recognised paradox that autotrophic ammonia oxidation occurs in acidic soils despite the fact that most cultivated ammonia oxidizing bacteria only grow at neutral pH.
  • Organisms with the domain Archaea (distinct from Bacteria and Eucarya) have recently been implicated in this essential biogeochemical.
  • This paper demonstrates for the first time that the recently discovered ammonia oxidising archaea are relatively more transcriptional active at low pH indicating that they could be primarily responsible for ammonia oxidation in acidic soils